Fix Clear Inheritance issues

editor/docks/scene_tree_dock.cpp

@@ -1396,7 +1396,8 @@ void SceneTreeDock::_tool_selected(int p_tool, bool p_confirm_override) {
 				Node *node = e->get();
 				if (node) {
 					node->set_scene_inherited_state(Ref<SceneState>());
-					scene_tree->update_tree();
+					editor_data->reload_scene_from_memory(editor_data->get_edited_scene(), true);
+					scene_tree->clear_cache();
 					InspectorDock::get_inspector_singleton()->update_tree();
 				}
 			}

editor/editor_data.cpp

@@ -706,40 +706,54 @@ bool EditorData::check_and_update_scene(int p_idx) {
 	bool must_reload = _find_updated_instances(edited_scene[p_idx].root, edited_scene[p_idx].root, checked_scenes);
 
 	if (must_reload) {
-		Ref<PackedScene> pscene;
-		pscene.instantiate();
-
-		EditorProgress ep("update_scene", TTR("Updating Scene"), 2);
-		ep.step(TTR("Storing local changes..."), 0);
-		// Pack first, so it stores diffs to previous version of saved scene.
-		Error err = pscene->pack(edited_scene[p_idx].root);
-		ERR_FAIL_COND_V(err != OK, false);
-		ep.step(TTR("Updating scene..."), 1);
-		Node *new_scene = pscene->instantiate(PackedScene::GEN_EDIT_STATE_MAIN);
-		ERR_FAIL_NULL_V(new_scene, false);
-
-		// Transfer selection.
-		List<Node *> new_selection;
-		for (const Node *E : edited_scene.write[p_idx].selection) {
-			NodePath p = edited_scene[p_idx].root->get_path_to(E);
-			Node *new_node = new_scene->get_node(p);
-			if (new_node) {
-				new_selection.push_back(new_node);
-			}
-		}
-
-		new_scene->set_scene_file_path(edited_scene[p_idx].root->get_scene_file_path());
-		Node *old_root = edited_scene[p_idx].root;
-		EditorNode::get_singleton()->set_edited_scene(new_scene);
-		memdelete(old_root);
-		edited_scene.write[p_idx].selection = new_selection;
+		reload_scene_from_memory(p_idx, false);
 
 		return true;
 	}
 
 	return false;
 }
 
+bool EditorData::reload_scene_from_memory(int p_idx, bool p_mark_unsaved) {
+	ERR_FAIL_INDEX_V(p_idx, edited_scene.size(), false);
+	if (!edited_scene[p_idx].root) {
+		return false;
+	}
+
+	Ref<PackedScene> pscene;
+	pscene.instantiate();
+
+	EditorProgress ep("update_scene", TTR("Updating Scene"), 2);
+	ep.step(TTR("Storing local changes..."), 0);
+	// Pack first, so it stores diffs to previous version of saved scene.
+	Error err = pscene->pack(edited_scene[p_idx].root);
+	ERR_FAIL_COND_V(err != OK, false);
+	ep.step(TTR("Updating scene..."), 1);
+	Node *new_scene = pscene->instantiate(PackedScene::GEN_EDIT_STATE_MAIN);
+	ERR_FAIL_NULL_V(new_scene, false);
+
+	// Transfer selection.
+	List<Node *> new_selection;
+	for (const Node *E : edited_scene.write[p_idx].selection) {
+		NodePath p = edited_scene[p_idx].root->get_path_to(E);
+		Node *new_node = new_scene->get_node(p);
+		if (new_node) {
+			new_selection.push_back(new_node);
+		}
+	}
+
+	new_scene->set_scene_file_path(edited_scene[p_idx].root->get_scene_file_path());
+	Node *old_root = edited_scene[p_idx].root;
+	EditorNode::get_singleton()->set_edited_scene(new_scene);
+	memdelete(old_root);
+	edited_scene.write[p_idx].selection = new_selection;
+
+	if (p_mark_unsaved) {
+		EditorUndoRedoManager::get_singleton()->clear_history(get_scene_history_id(p_idx));
+	}
+	return true;
+}
+
 int EditorData::get_edited_scene() const {
 	return current_edited_scene;
 }

editor/editor_data.h

@@ -219,6 +219,7 @@ class EditorData {
 	void set_edited_scene_live_edit_root(const NodePath &p_root);
 	NodePath get_edited_scene_live_edit_root();
 	bool check_and_update_scene(int p_idx);
+	bool reload_scene_from_memory(int p_idx, bool p_mark_unsaved);
 	void move_edited_scene_to_index(int p_idx);
 
 	bool call_build();

editor/scene/scene_tree_editor.cpp

@@ -1728,13 +1728,17 @@ void SceneTreeEditor::set_display_foreign_nodes(bool p_display) {
 	_update_tree();
 }
 
-void SceneTreeEditor::set_valid_types(const Vector<StringName> &p_valid) {
-	valid_types = p_valid;
+void SceneTreeEditor::clear_cache() {
 	node_cache.force_update = true;
 	callable_mp(this, &SceneTreeEditor::_update_tree).call_deferred(false);
 	tree_dirty = true;
 }
 
+void SceneTreeEditor::set_valid_types(const Vector<StringName> &p_valid) {
+	valid_types = p_valid;
+	clear_cache();
+}
+
 void SceneTreeEditor::set_editor_selection(EditorSelection *p_selection) {
 	editor_selection = p_selection;
 	tree->set_select_mode(Tree::SELECT_MULTI);

editor/scene/scene_tree_editor.h

@@ -248,6 +248,7 @@ class SceneTreeEditor : public Control {
 
 	void set_show_enabled_subscene(bool p_show) { show_enabled_subscene = p_show; }
 	void set_valid_types(const Vector<StringName> &p_valid);
+	void clear_cache();
 
 	inline void update_tree() { _update_tree(); }