diff --git a/editor/scene_tree_dock.cpp b/editor/scene_tree_dock.cpp
index a38487635fb1..9d69addc12c6 100644
--- a/editor/scene_tree_dock.cpp
+++ b/editor/scene_tree_dock.cpp
@@ -1635,10 +1635,15 @@ bool SceneTreeDock::_update_node_path(Node *p_root_node, NodePath &r_node_path,
 	return false;
 }
 
-bool SceneTreeDock::_check_node_path_recursive(Node *p_root_node, Variant &r_variant, HashMap<Node *, NodePath> *p_renames) const {
+bool SceneTreeDock::_check_node_path_recursive(Node *p_root_node, Variant &r_variant, HashMap<Node *, NodePath> *p_renames, bool p_inside_resource) const {
 	switch (r_variant.get_type()) {
 		case Variant::NODE_PATH: {
 			NodePath node_path = r_variant;
+			if (p_inside_resource && !p_root_node->has_node(node_path)) {
+				// Resources may have NodePaths to nodes that aren't on the scene, so skip them.
+				return false;
+			}
+
 			if (!node_path.is_empty() && _update_node_path(p_root_node, node_path, p_renames)) {
 				r_variant = node_path;
 				return true;
@@ -1650,7 +1655,7 @@ bool SceneTreeDock::_check_node_path_recursive(Node *p_root_node, Variant &r_var
 			bool updated = false;
 			for (int i = 0; i < a.size(); i++) {
 				Variant value = a[i];
-				if (_check_node_path_recursive(p_root_node, value, p_renames)) {
+				if (_check_node_path_recursive(p_root_node, value, p_renames, p_inside_resource)) {
 					if (!updated) {
 						a = a.duplicate(); // Need to duplicate for undo-redo to work.
 						updated = true;
@@ -1669,7 +1674,7 @@ bool SceneTreeDock::_check_node_path_recursive(Node *p_root_node, Variant &r_var
 			bool updated = false;
 			for (int i = 0; i < d.size(); i++) {
 				Variant value = d.get_value_at_index(i);
-				if (_check_node_path_recursive(p_root_node, value, p_renames)) {
+				if (_check_node_path_recursive(p_root_node, value, p_renames, p_inside_resource)) {
 					if (!updated) {
 						d = d.duplicate(); // Need to duplicate for undo-redo to work.
 						updated = true;
@@ -1699,7 +1704,7 @@ bool SceneTreeDock::_check_node_path_recursive(Node *p_root_node, Variant &r_var
 				String propertyname = E.name;
 				Variant old_variant = resource->get(propertyname);
 				Variant updated_variant = old_variant;
-				if (_check_node_path_recursive(p_root_node, updated_variant, p_renames)) {
+				if (_check_node_path_recursive(p_root_node, updated_variant, p_renames, true)) {
 					EditorUndoRedoManager *undo_redo = EditorUndoRedoManager::get_singleton();
 					undo_redo->add_do_property(resource, propertyname, updated_variant);
 					undo_redo->add_undo_property(resource, propertyname, old_variant);
diff --git a/editor/scene_tree_dock.h b/editor/scene_tree_dock.h
index 9c111bce71fa..3f02d2881de1 100644
--- a/editor/scene_tree_dock.h
+++ b/editor/scene_tree_dock.h
@@ -281,7 +281,7 @@ class SceneTreeDock : public VBoxContainer {
 	static void _update_configuration_warning();
 
 	bool _update_node_path(Node *p_root_node, NodePath &r_node_path, HashMap<Node *, NodePath> *p_renames) const;
-	bool _check_node_path_recursive(Node *p_root_node, Variant &r_variant, HashMap<Node *, NodePath> *p_renames) const;
+	bool _check_node_path_recursive(Node *p_root_node, Variant &r_variant, HashMap<Node *, NodePath> *p_renames, bool p_inside_resource = false) const;
 	bool _check_node_recursive(Variant &r_variant, Node *p_node, Node *p_by_node, const String type_hint, String &r_warn_message);
 	void _replace_node(Node *p_node, Node *p_by_node, bool p_keep_properties = true, bool p_remove_old = true);