diff --git a/src/platform/packages/shared/presentation/presentation_containers/interfaces/unsaved_changes/initialize_unsaved_changes.ts b/src/platform/packages/shared/presentation/presentation_containers/interfaces/unsaved_changes/initialize_unsaved_changes.ts
index 1038ef8c9c889..af3be9f653119 100644
--- a/src/platform/packages/shared/presentation/presentation_containers/interfaces/unsaved_changes/initialize_unsaved_changes.ts
+++ b/src/platform/packages/shared/presentation/presentation_containers/interfaces/unsaved_changes/initialize_unsaved_changes.ts
@@ -16,9 +16,9 @@ import {
 } from '@kbn/presentation-publishing';
 import { MaybePromise } from '@kbn/utility-types';
 import { Observable, combineLatestWith, debounceTime, map, of } from 'rxjs';
+import { isEqual, sortBy } from 'lodash';
 import { apiHasLastSavedChildState } from '../last_saved_child_state';
 import { PresentationContainer } from '../presentation_container';
-
 const UNSAVED_CHANGES_DEBOUNCE = 100;
 
 export const initializeUnsavedChanges = <StateType extends object = object>({
@@ -29,6 +29,7 @@ export const initializeUnsavedChanges = <StateType extends object = object>({
   defaultState,
   serializeState,
   anyStateChange$,
+  checkRefEquality,
 }: {
   uuid: string;
   parentApi: unknown;
@@ -37,6 +38,7 @@ export const initializeUnsavedChanges = <StateType extends object = object>({
   getComparators: () => StateComparators<StateType>;
   defaultState?: Partial<StateType>;
   onReset: (lastSavedPanelState?: SerializedPanelState<StateType>) => MaybePromise<void>;
+  checkRefEquality?: boolean;
 }): PublishesUnsavedChanges => {
   if (!apiHasLastSavedChildState<StateType>(parentApi)) {
     return {
@@ -46,16 +48,25 @@ export const initializeUnsavedChanges = <StateType extends object = object>({
   }
 
   const hasUnsavedChanges$ = anyStateChange$.pipe(
-    combineLatestWith(
-      parentApi.lastSavedStateForChild$(uuid).pipe(map((panelState) => panelState?.rawState))
-    ),
+    combineLatestWith(parentApi.lastSavedStateForChild$(uuid)),
     debounceTime(UNSAVED_CHANGES_DEBOUNCE),
     map(([, lastSavedState]) => {
-      const currentState = serializeState().rawState;
+      const currentState = serializeState();
+
+      // check ref equality
+      if (checkRefEquality) {
+        const lastSavedRefs = sortBy(lastSavedState?.references ?? [], 'id');
+        const currentRefs = sortBy(currentState?.references ?? [], 'id');
+        const equalRefs = isEqual(lastSavedRefs, currentRefs);
+
+        if (!equalRefs) return true;
+      }
+
+      // check state equality
       return !areComparatorsEqual(
         getComparators(),
-        lastSavedState,
-        currentState,
+        lastSavedState?.rawState,
+        currentState.rawState,
         defaultState,
         (key: string) => {
           const childApi = (parentApi as Partial<PresentationContainer>).children$?.getValue()[
diff --git a/src/platform/plugins/shared/dashboard/public/dashboard_api/get_dashboard_api.ts b/src/platform/plugins/shared/dashboard/public/dashboard_api/get_dashboard_api.ts
index 2aaebe1f2f568..fb32970c265a9 100644
--- a/src/platform/plugins/shared/dashboard/public/dashboard_api/get_dashboard_api.ts
+++ b/src/platform/plugins/shared/dashboard/public/dashboard_api/get_dashboard_api.ts
@@ -174,6 +174,7 @@ export function getDashboardApi({
       }
 
       if (saveResult) {
+        references$.next(saveResult.references);
         unsavedChangesManager.internalApi.onSave(saveResult.savedState);
         const settings = settingsManager.api.getSettings();
         settingsManager.api.setSettings({
@@ -185,8 +186,6 @@ export function getDashboardApi({
           title: saveResult.savedState.title,
         });
         savedObjectId$.next(saveResult.id);
-
-        references$.next(saveResult.references);
       }
 
       return saveResult;
@@ -203,8 +202,8 @@ export function getDashboardApi({
       });
 
       if (saveResult?.error) return;
-      unsavedChangesManager.internalApi.onSave(dashboardState);
       references$.next(saveResult.references);
+      unsavedChangesManager.internalApi.onSave(dashboardState);
 
       return;
     },
diff --git a/src/platform/plugins/shared/visualizations/public/embeddable/visualize_embeddable.tsx b/src/platform/plugins/shared/visualizations/public/embeddable/visualize_embeddable.tsx
index 4642cca35f810..61fc6fb21827f 100644
--- a/src/platform/plugins/shared/visualizations/public/embeddable/visualize_embeddable.tsx
+++ b/src/platform/plugins/shared/visualizations/public/embeddable/visualize_embeddable.tsx
@@ -177,6 +177,7 @@ export const getVisualizeEmbeddableFactory: (deps: {
       serializeState: () => {
         return serializeVisualizeEmbeddable(savedObjectId$.getValue(), linkedToLibrary);
       },
+      checkRefEquality: true,
       anyStateChange$: merge(
         ...(dynamicActionsManager ? [dynamicActionsManager.anyStateChange$] : []),
         savedObjectId$,
diff --git a/src/platform/test/functional/fixtures/kbn_archiver/dashboard/current/kibana.json b/src/platform/test/functional/fixtures/kbn_archiver/dashboard/current/kibana.json
index e453c2ba30311..65411f092c3c7 100644
--- a/src/platform/test/functional/fixtures/kbn_archiver/dashboard/current/kibana.json
+++ b/src/platform/test/functional/fixtures/kbn_archiver/dashboard/current/kibana.json
@@ -3198,6 +3198,11 @@
       "type": "visualization",
       "id": "50643b60-3dd3-11e8-b2b9-5d5dc1715159"
     },
+    {
+      "name":"ffc13252-56b4-4e3f-847e-61373fa0be86:kibanaSavedObjectMeta.searchSourceJSON.index",
+      "type":"index-pattern",
+      "id":"a0f483a0-3dc9-11e8-8660-4d65aa086b3c"
+    },
     {
       "name": "controlGroup_41827e70-5285-4d44-8375-4c498449b9a7:optionsListControlDataView",
       "type": "index-pattern",
@@ -3317,4 +3322,4 @@
   "managed": false,
   "coreMigrationVersion": "8.8.0",
   "typeMigrationVersion": "10.2.0"
-}
\ No newline at end of file
+}