diff --git a/scene/resources/packed_scene.cpp b/scene/resources/packed_scene.cpp
index 4d19e4727b9..c777dfc440c 100644
--- a/scene/resources/packed_scene.cpp
+++ b/scene/resources/packed_scene.cpp
@@ -393,7 +393,15 @@ Error SceneState::_parse_node(Node *p_owner, Node *p_node, int p_parent_idx, Map
 
 	nd.name = _nm_get_string(p_node->get_name(), name_map);
 	nd.instance = -1; //not instanced by default
-	nd.index = p_node->get_index();
+
+	//really convoluted condition, but it basically checks that index is only saved when part of an inherited scene OR the node parent is from the edited scene
+	if (p_owner->get_scene_inherited_state().is_null() && (p_node == p_owner || (p_node->get_owner() == p_owner && (p_node->get_parent() == p_owner || p_node->get_parent()->get_owner() == p_owner)))) {
+		//do not save index, because it belongs to saved scene and scene is not inherited
+		nd.index = -1;
+	} else {
+		//part of an inherited scene, or parent is from an instanced scene
+		nd.index = p_node->get_index();
+	}
 
 	// if this node is part of an instanced scene or sub-instanced scene
 	// we need to get the corresponding instance states.