### 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 (path.size() == 0) {
		return nullptr;
	}
	EditorFileSystemDirectory *fs = filesystem;
	for (int i = 0; i < path.size(); i++) {
		int idx = -1;
		for (int j = 0; j < fs->get_subdir_count(); j++) {
			if (fs->get_subdir(j)->get_name() == path[i]) {
				idx = j;
				break;
			}
		}
		if (idx == -1) {
			return nullptr;
		} else {
			fs = fs->get_subdir(idx);
		}
	}
	return fs;
}
void EditorFileSystem::_save_late_updated_files() {
	
	String fscache = EditorPaths::get_singleton()->get_project_settings_dir().path_join("filesystem_update4");
	Ref<FileAccess> f = FileAccess::open(fscache, FileAccess::WRITE);
	ERR_FAIL_COND_MSG(f.is_null(), "Cannot create file '" + fscache + "'. Check user write permissions.");
	for (const String &E : late_update_files) {
		f->store_line(E);
	}
}
Vector<String> EditorFileSystem::_get_dependencies(const String &p_path) {