diff --git a/packages/block-editor/src/components/provider/use-block-sync.js b/packages/block-editor/src/components/provider/use-block-sync.js
index 57e53979142d6..300c108a70cf1 100644
--- a/packages/block-editor/src/components/provider/use-block-sync.js
+++ b/packages/block-editor/src/components/provider/use-block-sync.js
@@ -2,7 +2,7 @@
  * WordPress dependencies
  */
 import { useEffect, useRef } from '@wordpress/element';
-import { useRegistry } from '@wordpress/data';
+import { useRegistry, useSelect } from '@wordpress/data';
 import { cloneBlock } from '@wordpress/blocks';
 
 /**
@@ -82,6 +82,15 @@ export default function useBlockSync( {
 	} = registry.dispatch( blockEditorStore );
 	const { getBlockName, getBlocks, getSelectionStart, getSelectionEnd } =
 		registry.select( blockEditorStore );
+	const isControlled = useSelect(
+		( select ) => {
+			return (
+				! clientId ||
+				select( blockEditorStore ).areInnerBlocksControlled( clientId )
+			);
+		},
+		[ clientId ]
+	);
 
 	const pendingChanges = useRef( { incoming: null, outgoing: [] } );
 	const subscribed = useRef( false );
@@ -177,6 +186,23 @@ export default function useBlockSync( {
 		}
 	}, [ controlledBlocks, clientId ] );
 
+	const isMounted = useRef( false );
+
+	useEffect( () => {
+		// On mount, controlled blocks are already set in the effect above.
+		if ( ! isMounted.current ) {
+			isMounted.current = true;
+			return;
+		}
+
+		// When the block becomes uncontrolled, it means its inner state has been reset
+		// we need to take the blocks again from the external value property.
+		if ( ! isControlled ) {
+			pendingChanges.current.outgoing = [];
+			setControlledBlocks();
+		}
+	}, [ isControlled ] );
+
 	useEffect( () => {
 		const {
 			getSelectedBlocksInitialCaretPosition,
diff --git a/test/e2e/specs/site-editor/undo.spec.js b/test/e2e/specs/site-editor/undo.spec.js
new file mode 100644
index 0000000000000..17c4e4ada6e61
--- /dev/null
+++ b/test/e2e/specs/site-editor/undo.spec.js
@@ -0,0 +1,42 @@
+/**
+ * WordPress dependencies
+ */
+const { test, expect } = require( '@wordpress/e2e-test-utils-playwright' );
+
+test.describe( 'undo', () => {
+	test.beforeAll( async ( { requestUtils } ) => {
+		await requestUtils.activateTheme( 'emptytheme' );
+	} );
+
+	test.afterAll( async ( { requestUtils } ) => {
+		await requestUtils.activateTheme( 'twentytwentyone' );
+	} );
+
+	test( 'does not empty header', async ( { admin, page, editor } ) => {
+		await admin.visitSiteEditor( { canvas: 'edit' } );
+
+		// Check if there's a valid child block with a type (not appender).
+		await expect(
+			editor.canvas.locator(
+				'[data-type="core/template-part"] [data-type]'
+			)
+		).not.toHaveCount( 0 );
+
+		// insert a block
+		await editor.insertBlock( { name: 'core/paragraph' } );
+
+		// undo
+		await page
+			.getByRole( 'button', {
+				name: 'Undo',
+			} )
+			.click();
+
+		// Check if there's a valid child block with a type (not appender).
+		await expect(
+			editor.canvas.locator(
+				'[data-type="core/template-part"] [data-type]'
+			)
+		).not.toHaveCount( 0 );
+	} );
+} );