diff --git a/superset-frontend/src/dashboard/components/DashboardBuilder/DashboardContainer.test.tsx b/superset-frontend/src/dashboard/components/DashboardBuilder/DashboardContainer.test.tsx
new file mode 100644
index 00000000000..126b25d3458
--- /dev/null
+++ b/superset-frontend/src/dashboard/components/DashboardBuilder/DashboardContainer.test.tsx
@@ -0,0 +1,389 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+import { render, waitFor } from 'spec/helpers/testing-library';
+import fetchMock from 'fetch-mock';
+import { storeWithState } from 'spec/fixtures/mockStore';
+import mockState from 'spec/fixtures/mockState';
+import { sliceId } from 'spec/fixtures/mockChartQueries';
+import { NativeFilterType } from '@superset-ui/core';
+import { CHART_TYPE } from '../../util/componentTypes';
+import DashboardContainer from './DashboardContainer';
+import * as nativeFiltersActions from '../../actions/nativeFilters';
+
+fetchMock.get('glob:*/csstemplateasyncmodelview/api/read', {});
+fetchMock.put('glob:*/api/v1/dashboard/*/colors*', {});
+fetchMock.post('glob:*/superset/log/?*', {});
+
+jest.mock('@visx/responsive', () => ({
+  ParentSize: ({
+    children,
+  }: {
+    children: (props: { width: number }) => JSX.Element;
+  }) => children({ width: 800 }),
+}));
+
+jest.mock('src/dashboard/containers/DashboardGrid', () => ({
+  __esModule: true,
+  default: () => <div data-test="mock-dashboard-grid" />,
+}));
+
+function createTestState(overrides = {}) {
+  return {
+    ...mockState,
+    dashboardState: {
+      ...mockState.dashboardState,
+      sliceIds: [sliceId],
+    },
+    dashboardLayout: {
+      ...mockState.dashboardLayout,
+      present: {
+        ...mockState.dashboardLayout.present,
+        CHART_ID: {
+          id: 'CHART_ID',
+          type: CHART_TYPE,
+          meta: {
+            chartId: sliceId,
+            width: 4,
+            height: 10,
+          },
+          parents: ['ROOT_ID', 'GRID_ID', 'ROW_ID'],
+        },
+      },
+    },
+    nativeFilters: {
+      filters: {
+        'FILTER-1': {
+          id: 'FILTER-1',
+          name: 'Test Filter',
+          filterType: 'filter_select',
+          targets: [
+            {
+              datasetId: 1,
+              column: { name: 'country' },
+            },
+          ],
+          defaultDataMask: {
+            filterState: { value: null },
+          },
+          cascadeParentIds: [],
+          scope: {
+            rootPath: ['ROOT_ID'],
+            excluded: [],
+          },
+          controlValues: {},
+          type: NativeFilterType.NativeFilter,
+        },
+      },
+    },
+    ...overrides,
+  };
+}
+
+function setup(overrideState = {}) {
+  const initialState = createTestState(overrideState);
+  return render(<DashboardContainer />, {
+    useRedux: true,
+    store: storeWithState(initialState),
+  });
+}
+
+function setupWithStore(overrideState = {}) {
+  const initialState = createTestState(overrideState);
+  const store = storeWithState(initialState);
+  const renderResult = render(<DashboardContainer />, {
+    useRedux: true,
+    store,
+  });
+  return { store, ...renderResult };
+}
+
+let setInScopeStatusMock: jest.SpyInstance;
+
+beforeEach(() => {
+  setInScopeStatusMock = jest.spyOn(
+    nativeFiltersActions,
+    'setInScopeStatusOfFilters',
+  );
+  setInScopeStatusMock.mockReturnValue(jest.fn());
+});
+
+afterEach(() => {
+  setInScopeStatusMock.mockRestore();
+});
+
+test('calculates chartsInScope correctly for filters', async () => {
+  setup();
+
+  await waitFor(() => {
+    expect(setInScopeStatusMock).toHaveBeenCalled();
+  });
+
+  expect(setInScopeStatusMock).toHaveBeenCalledWith(
+    expect.arrayContaining([
+      expect.objectContaining({
+        filterId: 'FILTER-1',
+        chartsInScope: [sliceId],
+      }),
+    ]),
+  );
+});
+
+test('recalculates chartsInScope when filter non-scope properties change', async () => {
+  const { store } = setupWithStore();
+
+  await waitFor(() => {
+    expect(setInScopeStatusMock).toHaveBeenCalled();
+  });
+
+  setInScopeStatusMock.mockClear();
+
+  // Bug scenario: Editing non-scope properties (e.g., "Sort filter values")
+  // triggers backend save, but response lacks chartsInScope.
+  // The fix ensures useEffect recalculates chartsInScope anyway.
+  const initialState = store.getState();
+  store.dispatch({
+    type: 'SET_NATIVE_FILTERS_CONFIG_COMPLETE',
+    filterChanges: [
+      {
+        ...initialState.nativeFilters.filters['FILTER-1'],
+        controlValues: {
+          ...initialState.nativeFilters.filters['FILTER-1'].controlValues,
+          sortAscending: false,
+        },
+      },
+    ],
+  });
+
+  await waitFor(() => {
+    expect(setInScopeStatusMock).toHaveBeenCalled();
+  });
+});
+
+test('handles multiple filters with different scopes', async () => {
+  const baseDashboardLayout = mockState.dashboardLayout.present;
+  // eslint-disable-next-line @typescript-eslint/no-unused-vars
+  const { CHART_ID: _removed, ...cleanLayout } = baseDashboardLayout;
+
+  const stateWithMultipleFilters = {
+    ...mockState,
+    dashboardState: {
+      ...mockState.dashboardState,
+      sliceIds: [18, 19],
+    },
+    dashboardLayout: {
+      ...mockState.dashboardLayout,
+      present: {
+        ...cleanLayout,
+        CHART_ID_1: {
+          id: 'CHART_ID_1',
+          type: CHART_TYPE,
+          meta: { chartId: 18, width: 4, height: 10 },
+          parents: ['ROOT_ID', 'GRID_ID', 'ROW_ID'],
+        },
+        CHART_ID_2: {
+          id: 'CHART_ID_2',
+          type: CHART_TYPE,
+          meta: { chartId: 19, width: 4, height: 10 },
+          parents: ['ROOT_ID', 'GRID_ID', 'ROW_ID'],
+        },
+      },
+    },
+    nativeFilters: {
+      filters: {
+        'FILTER-1': {
+          id: 'FILTER-1',
+          name: 'Filter 1',
+          filterType: 'filter_select',
+          targets: [{ datasetId: 1, column: { name: 'country' } }],
+          scope: { rootPath: ['ROOT_ID'], excluded: [] },
+          controlValues: {},
+          type: NativeFilterType.NativeFilter,
+        },
+        'FILTER-2': {
+          id: 'FILTER-2',
+          name: 'Filter 2',
+          filterType: 'filter_select',
+          targets: [{ datasetId: 1, column: { name: 'region' } }],
+          scope: { rootPath: ['ROOT_ID'], excluded: [19] },
+          controlValues: {},
+          type: NativeFilterType.NativeFilter,
+        },
+      },
+    },
+  };
+
+  setup(stateWithMultipleFilters);
+
+  await waitFor(() => {
+    expect(setInScopeStatusMock).toHaveBeenCalled();
+  });
+
+  expect(setInScopeStatusMock).toHaveBeenCalledWith(
+    expect.arrayContaining([
+      expect.objectContaining({
+        filterId: 'FILTER-1',
+        chartsInScope: expect.arrayContaining([18, 19]),
+      }),
+      expect.objectContaining({
+        filterId: 'FILTER-2',
+        chartsInScope: [18],
+      }),
+    ]),
+  );
+});
+
+test('handles filters with no charts in scope', async () => {
+  const stateWithExcludedFilter = createTestState({
+    nativeFilters: {
+      filters: {
+        'FILTER-1': {
+          id: 'FILTER-1',
+          name: 'Excluded Filter',
+          filterType: 'filter_select',
+          targets: [{ datasetId: 1, column: { name: 'country' } }],
+          scope: {
+            rootPath: ['ROOT_ID'],
+            excluded: [sliceId],
+          },
+          controlValues: {},
+          type: NativeFilterType.NativeFilter,
+        },
+      },
+    },
+  });
+
+  setup(stateWithExcludedFilter);
+
+  await waitFor(() => {
+    expect(setInScopeStatusMock).toHaveBeenCalled();
+  });
+
+  expect(setInScopeStatusMock).toHaveBeenCalledWith(
+    expect.arrayContaining([
+      expect.objectContaining({
+        filterId: 'FILTER-1',
+        chartsInScope: [],
+      }),
+    ]),
+  );
+});
+
+test('does not dispatch when there are no filters', () => {
+  const stateWithoutFilters = createTestState({
+    nativeFilters: {
+      filters: {},
+    },
+  });
+
+  setup(stateWithoutFilters);
+
+  expect(setInScopeStatusMock).not.toHaveBeenCalled();
+});
+
+test('calculates tabsInScope for filters with tab-scoped charts', async () => {
+  const baseDashboardLayout = mockState.dashboardLayout.present;
+  // eslint-disable-next-line @typescript-eslint/no-unused-vars
+  const { CHART_ID: _removed, ...cleanLayout } = baseDashboardLayout;
+
+  const stateWithTabs = {
+    ...mockState,
+    dashboardState: {
+      ...mockState.dashboardState,
+      sliceIds: [20, 21, 22],
+    },
+    dashboardLayout: {
+      ...mockState.dashboardLayout,
+      present: {
+        ...cleanLayout,
+        ROOT_ID: {
+          id: 'ROOT_ID',
+          type: 'ROOT',
+          children: ['TABS-1'],
+        },
+        'TABS-1': {
+          id: 'TABS-1',
+          type: 'TABS',
+          children: ['TAB-A', 'TAB-B'],
+          parents: ['ROOT_ID'],
+        },
+        'TAB-A': {
+          id: 'TAB-A',
+          type: 'TAB',
+          children: ['CHART-A1', 'CHART-A2'],
+          parents: ['ROOT_ID', 'TABS-1'],
+          meta: { text: 'Tab A' },
+        },
+        'TAB-B': {
+          id: 'TAB-B',
+          type: 'TAB',
+          children: ['CHART-B1'],
+          parents: ['ROOT_ID', 'TABS-1'],
+          meta: { text: 'Tab B' },
+        },
+        'CHART-A1': {
+          id: 'CHART-A1',
+          type: CHART_TYPE,
+          meta: { chartId: 20, width: 4, height: 10 },
+          parents: ['ROOT_ID', 'TABS-1', 'TAB-A'],
+        },
+        'CHART-A2': {
+          id: 'CHART-A2',
+          type: CHART_TYPE,
+          meta: { chartId: 21, width: 4, height: 10 },
+          parents: ['ROOT_ID', 'TABS-1', 'TAB-A'],
+        },
+        'CHART-B1': {
+          id: 'CHART-B1',
+          type: CHART_TYPE,
+          meta: { chartId: 22, width: 4, height: 10 },
+          parents: ['ROOT_ID', 'TABS-1', 'TAB-B'],
+        },
+      },
+    },
+    nativeFilters: {
+      filters: {
+        'FILTER-TAB-SCOPED': {
+          id: 'FILTER-TAB-SCOPED',
+          name: 'Tab Scoped Filter',
+          filterType: 'filter_select',
+          targets: [{ datasetId: 1, column: { name: 'region' } }],
+          scope: { rootPath: ['ROOT_ID'], excluded: [22] },
+          controlValues: {},
+          type: NativeFilterType.NativeFilter,
+        },
+      },
+    },
+  };
+
+  setup(stateWithTabs);
+
+  await waitFor(() => {
+    expect(setInScopeStatusMock).toHaveBeenCalled();
+  });
+
+  expect(setInScopeStatusMock).toHaveBeenCalledWith(
+    expect.arrayContaining([
+      expect.objectContaining({
+        filterId: 'FILTER-TAB-SCOPED',
+        chartsInScope: expect.arrayContaining([20, 21]),
+        tabsInScope: expect.arrayContaining(['TAB-A']),
+      }),
+    ]),
+  );
+});
diff --git a/superset-frontend/src/dashboard/components/DashboardBuilder/DashboardContainer.tsx b/superset-frontend/src/dashboard/components/DashboardBuilder/DashboardContainer.tsx
index 9ff41a99c29..10e3379f907 100644
--- a/superset-frontend/src/dashboard/components/DashboardBuilder/DashboardContainer.tsx
+++ b/superset-frontend/src/dashboard/components/DashboardBuilder/DashboardContainer.tsx
@@ -103,6 +103,9 @@ const TOP_OF_PAGE_RANGE = 220;
 
 const DashboardContainer: FC<DashboardContainerProps> = ({ topLevelTabs }) => {
   const nativeFilterScopes = useNativeFilterScopes();
+  const nativeFilters = useSelector<RootState, Filters>(
+    state => state.nativeFilters?.filters,
+  );
   const dispatch = useDispatch();
 
   const dashboardLayout = useSelector<RootState, DashboardLayout>(
@@ -192,7 +195,13 @@ const DashboardContainer: FC<DashboardContainerProps> = ({ topLevelTabs }) => {
       };
     });
     dispatch(setInScopeStatusOfFilters(scopes));
-  }, [chartIds, JSON.stringify(nativeFilterScopes), dashboardLayout, dispatch]);
+  }, [
+    chartIds,
+    JSON.stringify(nativeFilterScopes),
+    dashboardLayout,
+    dispatch,
+    JSON.stringify(nativeFilters),
+  ]);
 
   const childIds: string[] = useMemo(
     () => (topLevelTabs ? topLevelTabs.children : [DASHBOARD_GRID_ID]),
diff --git a/superset-frontend/src/dashboard/components/nativeFilters/state.test.ts b/superset-frontend/src/dashboard/components/nativeFilters/state.test.ts
index 24cd92b99cf..693c7d374b2 100644
--- a/superset-frontend/src/dashboard/components/nativeFilters/state.test.ts
+++ b/superset-frontend/src/dashboard/components/nativeFilters/state.test.ts
@@ -39,90 +39,260 @@ beforeEach(() => {
   });
 });
 
-// eslint-disable-next-line no-restricted-globals -- TODO: Migrate from describe blocks
-describe('useIsFilterInScope', () => {
-  test('should return true for dividers (always in scope)', () => {
-    const divider: Divider = {
-      id: 'divider_1',
-      type: NativeFilterType.Divider,
-      title: 'Sample Divider',
-      description: 'Divider description',
-    };
+test('useIsFilterInScope should return true for dividers (always in scope)', () => {
+  const divider: Divider = {
+    id: 'divider_1',
+    type: NativeFilterType.Divider,
+    title: 'Sample Divider',
+    description: 'Divider description',
+  };
 
-    const { result } = renderHook(() => useIsFilterInScope());
-    expect(result.current(divider)).toBe(true);
-  });
+  const { result } = renderHook(() => useIsFilterInScope());
+  expect(result.current(divider)).toBe(true);
+});
 
-  test('should return true for filters with charts in active tabs', () => {
-    const filter: Filter = {
+test('useIsFilterInScope should return true for filters with charts in active tabs', () => {
+  const filter: Filter = {
+    id: 'filter_1',
+    name: 'Test Filter',
+    filterType: 'filter_select',
+    type: NativeFilterType.NativeFilter,
+    chartsInScope: [123],
+    scope: { rootPath: ['TAB_1'], excluded: [] },
+    controlValues: {},
+    defaultDataMask: {},
+    cascadeParentIds: [],
+    targets: [{ column: { name: 'column_name' }, datasetId: 1 }],
+    description: 'Sample filter description',
+  };
+
+  const { result } = renderHook(() => useIsFilterInScope());
+  expect(result.current(filter)).toBe(true);
+});
+
+test('useIsFilterInScope should return false for filters with inactive rootPath', () => {
+  const filter: Filter = {
+    id: 'filter_3',
+    name: 'Test Filter 3',
+    filterType: 'filter_select',
+    type: NativeFilterType.NativeFilter,
+    scope: { rootPath: ['TAB_99'], excluded: [] },
+    controlValues: {},
+    defaultDataMask: {},
+    cascadeParentIds: [],
+    targets: [{ column: { name: 'column_name' }, datasetId: 3 }],
+    description: 'Sample filter description',
+  };
+
+  const { result } = renderHook(() => useIsFilterInScope());
+  expect(result.current(filter)).toBe(false);
+});
+
+test('useSelectFiltersInScope should return all filters in scope when no tabs exist', () => {
+  const filters: Filter[] = [
+    {
       id: 'filter_1',
-      name: 'Test Filter',
+      name: 'Filter 1',
       filterType: 'filter_select',
       type: NativeFilterType.NativeFilter,
-      chartsInScope: [123],
-      scope: { rootPath: ['TAB_1'], excluded: [] },
+      scope: { rootPath: [], excluded: [] },
       controlValues: {},
       defaultDataMask: {},
       cascadeParentIds: [],
       targets: [{ column: { name: 'column_name' }, datasetId: 1 }],
       description: 'Sample filter description',
-    };
+    },
+    {
+      id: 'filter_2',
+      name: 'Filter 2',
+      filterType: 'filter_select',
+      type: NativeFilterType.NativeFilter,
+      scope: { rootPath: [], excluded: [] },
+      controlValues: {},
+      defaultDataMask: {},
+      cascadeParentIds: [],
+      targets: [{ column: { name: 'column_name' }, datasetId: 2 }],
+      description: 'Sample filter description',
+    },
+  ];
 
-    const { result } = renderHook(() => useIsFilterInScope());
-    expect(result.current(filter)).toBe(true);
+  const { result } = renderHook(() => useSelectFiltersInScope(filters));
+  expect(result.current[0]).toEqual(filters);
+  expect(result.current[1]).toEqual([]);
+});
+
+// Tests for filter scope persistence when chartsInScope is missing
+// (Bug fix: filters incorrectly marked out of scope after editing non-scope properties)
+test('filter without chartsInScope should fall back to rootPath check', () => {
+  (useSelector as jest.Mock).mockImplementation((selector: Function) => {
+    const mockState = {
+      dashboardState: { activeTabs: ['TAB_1'] },
+      dashboardLayout: { present: {} },
+    };
+    return selector(mockState);
   });
 
-  test('should return false for filters with inactive rootPath', () => {
-    const filter: Filter = {
-      id: 'filter_3',
-      name: 'Test Filter 3',
+  const filter: Filter = {
+    id: 'filter_fallback',
+    name: 'Filter Without Charts',
+    filterType: 'filter_select',
+    type: NativeFilterType.NativeFilter,
+    scope: { rootPath: ['TAB_1'], excluded: [] },
+    controlValues: {},
+    defaultDataMask: {},
+    cascadeParentIds: [],
+    targets: [{ column: { name: 'column_name' }, datasetId: 1 }],
+    description: 'Filter with missing chartsInScope',
+  };
+
+  const { result } = renderHook(() => useIsFilterInScope());
+  expect(result.current(filter)).toBe(true);
+});
+
+test('filter with empty chartsInScope array should check rootPath', () => {
+  (useSelector as jest.Mock).mockImplementation((selector: Function) => {
+    const mockState = {
+      dashboardState: { activeTabs: ['TAB_1'] },
+      dashboardLayout: { present: {} },
+    };
+    return selector(mockState);
+  });
+
+  const filter: Filter = {
+    id: 'filter_empty_charts',
+    name: 'Filter With Empty Charts',
+    filterType: 'filter_select',
+    type: NativeFilterType.NativeFilter,
+    chartsInScope: [],
+    scope: { rootPath: ['TAB_1'], excluded: [] },
+    controlValues: {},
+    defaultDataMask: {},
+    cascadeParentIds: [],
+    targets: [{ column: { name: 'column_name' }, datasetId: 1 }],
+    description: 'Filter with empty chartsInScope',
+  };
+
+  const { result } = renderHook(() => useIsFilterInScope());
+  expect(result.current(filter)).toBe(true);
+});
+
+test('filter without chartsInScope and inactive rootPath should be out of scope', () => {
+  (useSelector as jest.Mock).mockImplementation((selector: Function) => {
+    const mockState = {
+      dashboardState: { activeTabs: ['TAB_1'] },
+      dashboardLayout: { present: {} },
+    };
+    return selector(mockState);
+  });
+
+  const filter: Filter = {
+    id: 'filter_inactive',
+    name: 'Inactive Filter',
+    filterType: 'filter_select',
+    type: NativeFilterType.NativeFilter,
+    scope: { rootPath: ['INACTIVE_TAB'], excluded: [] },
+    controlValues: {},
+    defaultDataMask: {},
+    cascadeParentIds: [],
+    targets: [{ column: { name: 'column_name' }, datasetId: 1 }],
+    description: 'Filter in inactive tab',
+  };
+
+  const { result } = renderHook(() => useIsFilterInScope());
+  expect(result.current(filter)).toBe(false);
+});
+
+test('filter with ROOT_ID in rootPath should be in scope when chartsInScope is missing', () => {
+  (useSelector as jest.Mock).mockImplementation((selector: Function) => {
+    const mockState = {
+      dashboardState: { activeTabs: ['ROOT_ID'] },
+      dashboardLayout: { present: {} },
+    };
+    return selector(mockState);
+  });
+
+  const filter: Filter = {
+    id: 'filter_root',
+    name: 'Global Filter',
+    filterType: 'filter_select',
+    type: NativeFilterType.NativeFilter,
+    scope: { rootPath: ['ROOT_ID'], excluded: [] },
+    controlValues: {},
+    defaultDataMask: {},
+    cascadeParentIds: [],
+    targets: [{ column: { name: 'column_name' }, datasetId: 1 }],
+    description: 'Global filter with missing chartsInScope',
+  };
+
+  const { result } = renderHook(() => useIsFilterInScope());
+  expect(result.current(filter)).toBe(true);
+});
+
+test('useSelectFiltersInScope correctly categorizes filters with missing chartsInScope', () => {
+  (useSelector as jest.Mock).mockImplementation((selector: Function) => {
+    const mockState = {
+      dashboardState: { activeTabs: ['TAB_1'] },
+      dashboardLayout: {
+        present: {
+          tab1: { type: 'TAB', id: 'TAB_1' },
+        },
+      },
+    };
+    return selector(mockState);
+  });
+
+  const filters: Filter[] = [
+    {
+      id: 'filter_in_scope',
+      name: 'In Scope Filter',
+      filterType: 'filter_select',
+      type: NativeFilterType.NativeFilter,
+      scope: { rootPath: ['TAB_1'], excluded: [] },
+      controlValues: {},
+      defaultDataMask: {},
+      cascadeParentIds: [],
+      targets: [{ column: { name: 'column_name' }, datasetId: 1 }],
+      description: 'Filter that should be in scope',
+    },
+    {
+      id: 'filter_out_scope',
+      name: 'Out of Scope Filter',
       filterType: 'filter_select',
       type: NativeFilterType.NativeFilter,
       scope: { rootPath: ['TAB_99'], excluded: [] },
       controlValues: {},
       defaultDataMask: {},
       cascadeParentIds: [],
-      targets: [{ column: { name: 'column_name' }, datasetId: 3 }],
-      description: 'Sample filter description',
-    };
+      targets: [{ column: { name: 'column_name' }, datasetId: 2 }],
+      description: 'Filter that should be out of scope',
+    },
+  ];
 
-    const { result } = renderHook(() => useIsFilterInScope());
-    expect(result.current(filter)).toBe(false);
-  });
+  const { result } = renderHook(() => useSelectFiltersInScope(filters));
+
+  expect(result.current[0]).toContainEqual(
+    expect.objectContaining({ id: 'filter_in_scope' }),
+  );
+  expect(result.current[1]).toContainEqual(
+    expect.objectContaining({ id: 'filter_out_scope' }),
+  );
 });
 
-// eslint-disable-next-line no-restricted-globals -- TODO: Migrate from describe blocks
-describe('useSelectFiltersInScope', () => {
-  test('should return all filters in scope when no tabs exist', () => {
-    const filters: Filter[] = [
-      {
-        id: 'filter_1',
-        name: 'Filter 1',
-        filterType: 'filter_select',
-        type: NativeFilterType.NativeFilter,
-        scope: { rootPath: [], excluded: [] },
-        controlValues: {},
-        defaultDataMask: {},
-        cascadeParentIds: [],
-        targets: [{ column: { name: 'column_name' }, datasetId: 1 }],
-        description: 'Sample filter description',
-      },
-      {
-        id: 'filter_2',
-        name: 'Filter 2',
-        filterType: 'filter_select',
-        type: NativeFilterType.NativeFilter,
-        scope: { rootPath: [], excluded: [] },
-        controlValues: {},
-        defaultDataMask: {},
-        cascadeParentIds: [],
-        targets: [{ column: { name: 'column_name' }, datasetId: 2 }],
-        description: 'Sample filter description',
-      },
-    ];
+test('filter with chartsInScope takes precedence over rootPath', () => {
+  const filter: Filter = {
+    id: 'filter_priority',
+    name: 'Priority Filter',
+    filterType: 'filter_select',
+    type: NativeFilterType.NativeFilter,
+    chartsInScope: [123, 456],
+    scope: { rootPath: ['INACTIVE_TAB'], excluded: [] },
+    controlValues: {},
+    defaultDataMask: {},
+    cascadeParentIds: [],
+    targets: [{ column: { name: 'column_name' }, datasetId: 1 }],
+    description: 'Filter with chartsInScope should ignore rootPath',
+  };
 
-    const { result } = renderHook(() => useSelectFiltersInScope(filters));
-    expect(result.current[0]).toEqual(filters);
-    expect(result.current[1]).toEqual([]);
-  });
+  const { result } = renderHook(() => useIsFilterInScope());
+  expect(result.current(filter)).toBe(true);
 });
diff --git a/superset-frontend/src/dashboard/reducers/nativeFilters.test.ts b/superset-frontend/src/dashboard/reducers/nativeFilters.test.ts
new file mode 100644
index 00000000000..dc8b2a77fc8
--- /dev/null
+++ b/superset-frontend/src/dashboard/reducers/nativeFilters.test.ts
@@ -0,0 +1,162 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+import { Filter, NativeFilterType } from '@superset-ui/core';
+import nativeFilterReducer from './nativeFilters';
+import { SET_NATIVE_FILTERS_CONFIG_COMPLETE } from '../actions/nativeFilters';
+
+const createMockFilter = (
+  id: string,
+  chartsInScope?: number[],
+  tabsInScope?: string[],
+): Filter => ({
+  cascadeParentIds: [],
+  id,
+  name: `Filter ${id}`,
+  filterType: 'filter_select',
+  targets: [
+    {
+      datasetId: 0,
+      column: {
+        name: 'test column',
+        displayName: 'test column',
+      },
+    },
+  ],
+  defaultDataMask: {
+    filterState: {
+      value: null,
+    },
+  },
+  scope: {
+    rootPath: [],
+    excluded: [],
+  },
+  controlValues: {
+    allowsMultipleValues: true,
+    isRequired: false,
+  },
+  type: NativeFilterType.NativeFilter,
+  description: '',
+  chartsInScope,
+  tabsInScope,
+});
+
+test('SET_NATIVE_FILTERS_CONFIG_COMPLETE updates filters with complete scope properties', () => {
+  const initialState = {
+    filters: {
+      filter1: createMockFilter('filter1', [1, 2], ['tab1']),
+    },
+  };
+
+  const action = {
+    type: SET_NATIVE_FILTERS_CONFIG_COMPLETE as typeof SET_NATIVE_FILTERS_CONFIG_COMPLETE,
+    filterChanges: [createMockFilter('filter1', [3, 4], ['tab2'])],
+  };
+
+  const result = nativeFilterReducer(initialState, action);
+
+  expect(result.filters.filter1.chartsInScope).toEqual([3, 4]);
+  expect(result.filters.filter1.tabsInScope).toEqual(['tab2']);
+});
+
+test('SET_NATIVE_FILTERS_CONFIG_COMPLETE preserves existing chartsInScope when missing from update', () => {
+  const initialState = {
+    filters: {
+      filter1: createMockFilter('filter1', [1, 2, 3], ['tab1']),
+    },
+  };
+
+  const filterWithoutChartsInScope: Filter = {
+    ...createMockFilter('filter1', undefined, ['tab2']),
+    chartsInScope: undefined,
+  };
+
+  const action = {
+    type: SET_NATIVE_FILTERS_CONFIG_COMPLETE as typeof SET_NATIVE_FILTERS_CONFIG_COMPLETE,
+    filterChanges: [filterWithoutChartsInScope],
+  };
+
+  const result = nativeFilterReducer(initialState, action);
+
+  expect(result.filters.filter1.chartsInScope).toEqual([1, 2, 3]);
+  expect(result.filters.filter1.tabsInScope).toEqual(['tab2']);
+});
+
+test('SET_NATIVE_FILTERS_CONFIG_COMPLETE preserves existing tabsInScope when missing from update', () => {
+  const initialState = {
+    filters: {
+      filter1: createMockFilter('filter1', [1, 2], ['tab1', 'tab2']),
+    },
+  };
+
+  const filterWithoutTabsInScope: Filter = {
+    ...createMockFilter('filter1', [3, 4], undefined),
+    tabsInScope: undefined,
+  };
+
+  const action = {
+    type: SET_NATIVE_FILTERS_CONFIG_COMPLETE as typeof SET_NATIVE_FILTERS_CONFIG_COMPLETE,
+    filterChanges: [filterWithoutTabsInScope],
+  };
+
+  const result = nativeFilterReducer(initialState, action);
+
+  expect(result.filters.filter1.chartsInScope).toEqual([3, 4]);
+  expect(result.filters.filter1.tabsInScope).toEqual(['tab1', 'tab2']);
+});
+
+test('SET_NATIVE_FILTERS_CONFIG_COMPLETE handles undefined scope properties for new filters', () => {
+  const initialState = {
+    filters: {},
+  };
+
+  const filterWithUndefinedScopes: Filter = {
+    ...createMockFilter('filter1', undefined, undefined),
+    chartsInScope: undefined,
+    tabsInScope: undefined,
+  };
+
+  const action = {
+    type: SET_NATIVE_FILTERS_CONFIG_COMPLETE as typeof SET_NATIVE_FILTERS_CONFIG_COMPLETE,
+    filterChanges: [filterWithUndefinedScopes],
+  };
+
+  const result = nativeFilterReducer(initialState, action);
+
+  expect(result.filters.filter1.chartsInScope).toBeUndefined();
+  expect(result.filters.filter1.tabsInScope).toBeUndefined();
+});
+
+test('SET_NATIVE_FILTERS_CONFIG_COMPLETE treats empty arrays as valid scope properties', () => {
+  const initialState = {
+    filters: {
+      filter1: createMockFilter('filter1', [1, 2, 3], ['tab1', 'tab2']),
+    },
+  };
+
+  const action = {
+    type: SET_NATIVE_FILTERS_CONFIG_COMPLETE as typeof SET_NATIVE_FILTERS_CONFIG_COMPLETE,
+    filterChanges: [createMockFilter('filter1', [], [])],
+  };
+
+  const result = nativeFilterReducer(initialState, action);
+
+  expect(result.filters.filter1.chartsInScope).toEqual([]);
+  expect(result.filters.filter1.tabsInScope).toEqual([]);
+});
diff --git a/superset-frontend/src/dashboard/reducers/nativeFilters.ts b/superset-frontend/src/dashboard/reducers/nativeFilters.ts
index 6f225cb51b5..5161bb31d9e 100644
--- a/superset-frontend/src/dashboard/reducers/nativeFilters.ts
+++ b/superset-frontend/src/dashboard/reducers/nativeFilters.ts
@@ -69,7 +69,16 @@ function handleFilterChangesComplete(
 ) {
   const modifiedFilters = { ...state.filters };
   filters.forEach(filter => {
-    modifiedFilters[filter.id] = filter;
+    if (filter.chartsInScope != null && filter.tabsInScope != null) {
+      modifiedFilters[filter.id] = filter;
+    } else {
+      const existingFilter = modifiedFilters[filter.id];
+      modifiedFilters[filter.id] = {
+        ...filter,
+        chartsInScope: filter.chartsInScope ?? existingFilter?.chartsInScope,
+        tabsInScope: filter.tabsInScope ?? existingFilter?.tabsInScope,
+      };
+    }
   });
 
   return {