Thanks for the discussion. I think I found it, but it does feel like a hack. The more I think about the more I think I shouldn’t use Godots ResourceSaver.
Anyways… I can just set:
node.scene_file_path = “”
to be an empty String for all the children. This will prevent the reference to the PackedScene and save it as basically a new scene and the child nodes still have their references to the scripts.