diff --git a/editor/scene_tree_dock.cpp b/editor/scene_tree_dock.cpp
index 4d998118e2..8c6f1f5363 100644
--- a/editor/scene_tree_dock.cpp
+++ b/editor/scene_tree_dock.cpp
@@ -1824,7 +1824,6 @@ bool SceneTreeDock::_check_node_path_recursive(Node *p_root_node, Variant &r_var
 					EditorUndoRedoManager *undo_redo = EditorUndoRedoManager::get_singleton();
 					undo_redo->add_do_property(resource, propertyname, updated_variant);
 					undo_redo->add_undo_property(resource, propertyname, old_variant);
-					resource->set(propertyname, updated_variant);
 				}
 			}
 			break;
@@ -1968,7 +1967,6 @@ void SceneTreeDock::perform_node_renames(Node *p_base, HashMap<Node *, NodePath>
 			EditorUndoRedoManager *undo_redo = EditorUndoRedoManager::get_singleton();
 			undo_redo->add_do_property(p_base, propertyname, updated_variant);
 			undo_redo->add_undo_property(p_base, propertyname, old_variant);
-			p_base->set(propertyname, updated_variant);
 		}
 	}
 
@@ -2849,7 +2847,6 @@ void SceneTreeDock::perform_node_replace(Node *p_base, Node *p_node, Node *p_by_
 			EditorUndoRedoManager *undo_redo = EditorUndoRedoManager::get_singleton();
 			undo_redo->add_do_property(p_base, propertyname, updated_variant);
 			undo_redo->add_undo_property(p_base, propertyname, old_variant);
-			p_base->set(propertyname, updated_variant);
 			if (!warn_message.is_empty()) {
 				String node_path = (String(edited_scene->get_name()) + "/" + String(edited_scene->get_path_to(p_base))).trim_suffix("/.");
 				WARN_PRINT(warn_message + vformat("Removing the node from variable \"%s\" on node \"%s\".", propertyname, node_path));