### 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
res->set_edited(false);
	}
	for (const String &E : edited_resources) {
		Ref<Resource> res = ResourceCache::get_ref(E);
		if (!res.is_valid()) {
			continue; 
		}
		Ref<PackedScene> ps = res;
		if (ps.is_valid()) {
			continue; 
		}
		ResourceSaver::save(res, res->get_path(), flg);
		saved++;
	}
	EditorUndoRedoManager::get_singleton()->set_history_as_saved(EditorUndoRedoManager::GLOBAL_HISTORY);
	return saved;
}
static void _reset_animation_players(Node *p_node, List<Ref<AnimatedValuesBackup>> *r_anim_backups) {
	for (int i = 0; i < p_node->get_child_count(); i++) {
		AnimationPlayer *player = Object::cast_to<AnimationPlayer>(p_node->get_child(i));
		if (player && player->is_reset_on_save_enabled() && player->can_apply_reset()) {
			Ref<AnimatedValuesBackup> old_values = player->apply_reset();
			if (old_values.is_valid()) {
				r_anim_backups->push_back(old_values);
			}
		}
		_reset_animation_players(p_node->get_child(i), r_anim_backups);
	}
}
void EditorNode::_save_scene(String p_file, int idx) {