### Godot version

4.1 rc3

### System information

Windows 10.0.19045 - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1060 (NVIDIA; 30.0.15.1403) - Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz (8 Threads)

### Issue description

This™
![image](https://github.com/godotengine/godot/assets/2223172/cb33110f-a5b0-400a-951f-3fa425f05714)

It can still happen, but it's more difficult to trigger.

### Steps to reproduce

1. Create a new scene with a Control node
2. Add Theme to the Control
3. Open Theme Editor
4. Clear the `theme` property in Control
5. Save, with Theme Editor opened
6. Restart

### Minimal reproduction project

N/A
bool all_saved = true;
	for (int i = 0; i < editor_data.get_edited_scene_count(); i++) {
		Node *scene = editor_data.get_edited_scene_root(i);
		if (scene) {
			if (!scene->get_scene_file_path().is_empty() && DirAccess::exists(scene->get_scene_file_path().get_base_dir())) {
				if (i != editor_data.get_edited_scene()) {
					_save_scene(scene->get_scene_file_path(), i);
				} else {
					_save_scene_with_preview(scene->get_scene_file_path());
				}
			} else if (!scene->get_scene_file_path().is_empty()) {
				all_saved = false;
			}
		}
	}
	if (!all_saved) {
		show_warning(TTR("Could not save one or more scenes!"), TTR("Save All Scenes"));
	}
	save_default_environment();
}
void EditorNode::_mark_unsaved_scenes() {