diff --git a/editor/scene_tree_dock.cpp b/editor/scene_tree_dock.cpp
index 02c8a03ac6e..3110ecb9260 100644
--- a/editor/scene_tree_dock.cpp
+++ b/editor/scene_tree_dock.cpp
@@ -2650,6 +2650,13 @@ void SceneTreeDock::_delete_confirm(bool p_cut) {
 		}
 	}
 
+	if (!entire_scene) {
+		for (const Node *E : remove_list) {
+			// `move_child` + `get_index` doesn't really work for internal nodes.
+			ERR_FAIL_COND_MSG(E->get_internal_mode() != INTERNAL_MODE_DISABLED, "Trying to remove internal node, this is not supported.");
+		}
+	}
+
 	EditorNode::get_singleton()->hide_unused_editors(this);
 
 	EditorUndoRedoManager *undo_redo = EditorUndoRedoManager::get_singleton();
@@ -2662,10 +2669,6 @@ void SceneTreeDock::_delete_confirm(bool p_cut) {
 		undo_redo->add_undo_method(scene_tree, "update_tree");
 		undo_redo->add_undo_reference(edited_scene);
 	} else {
-		for (const Node *E : remove_list) {
-			// `move_child` + `get_index` doesn't really work for internal nodes.
-			ERR_FAIL_COND_MSG(E->get_internal_mode() != INTERNAL_MODE_DISABLED, "Trying to remove internal node, this is not supported.");
-		}
 		if (delete_tracks_checkbox->is_pressed() || p_cut) {
 			remove_list.sort_custom<Node::Comparator>(); // Sort nodes to keep positions.
 			HashMap<Node *, NodePath> path_renames;