### 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
if (p_res.is_null()) {
		return false;
	}
	if (processed.has(p_res)) {
		return processed[p_res];
	}
	bool changed = p_res->is_edited();
	p_res->set_edited(false);
	bool subchanged = _find_and_save_edited_subresources(p_res.ptr(), processed, flags);
	if (p_res->get_path().is_resource_file()) {
		if (changed || subchanged) {
			ResourceSaver::save(p_res, p_res->get_path(), flags);
		}
		processed[p_res] = false; 
		return false;
	} else {
		processed[p_res] = changed;
		return changed;
	}
}
bool EditorNode::_find_and_save_edited_subresources(Object *obj, HashMap<Ref<Resource>, bool> &processed, int32_t flags) {