### Godot version

v4.0.beta.custom_build [0a9e6e478]

### System information

Windows 10, Vulkan, GTX 960 528.24

### Issue description

This [55420](https://github.com/godotengine/godot/issues/55420) issue seems that it is not completely solved since in the advanced importer the same thing continues to happen.

### Steps to reproduce

- Put a 3D model on the scene
- Open the advanced import
- Disable Auto LOD or whatever you want to change
- See how mesh doesn't change

### Minimal reproduction project

N/A
if (FileAccess::exists(update_cache)) {
		{
			Ref<FileAccess> f2 = FileAccess::open(update_cache, FileAccess::READ);
			String l = f2->get_line().strip_edges();
			while (!l.is_empty()) {
				file_cache.erase(l); 
				l = f2->get_line().strip_edges();
			}
		}
		Ref<DirAccess> d = DirAccess::create(DirAccess::ACCESS_FILESYSTEM);
		d->remove(update_cache); 
	}
	EditorProgressBG scan_progress("efs", "ScanFS", 1000);
	ScanProgress sp;
	sp.low = 0;
	sp.hi = 1;
	sp.progress = &scan_progress;
	new_filesystem = memnew(EditorFileSystemDirectory);
	new_filesystem->parent = nullptr;
	Ref<DirAccess> d = DirAccess::create(DirAccess::ACCESS_RESOURCES);
	d->change_dir("res://");
	_scan_new_dir(new_filesystem, d, sp);
	file_cache.clear(); 
	if (!first_scan) {
		
		_save_filesystem_cache();
	}
	scanning = false;
}
void EditorFileSystem::_save_filesystem_cache() {