### 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 (dest_paths.size()) {
			md5s->store_line("dest_md5=\"" + FileAccess::get_multiple_md5(dest_paths) + "\"\n");
		}
	}
	
	fs->files[cpos]->modified_time = FileAccess::get_modified_time(p_file);
	fs->files[cpos]->import_modified_time = FileAccess::get_modified_time(p_file + ".import");
	fs->files[cpos]->deps = _get_dependencies(p_file);
	fs->files[cpos]->type = importer->get_resource_type();
	fs->files[cpos]->uid = uid;
	fs->files[cpos]->import_valid = fs->files[cpos]->type == "TextFile" ? true : ResourceLoader::is_import_valid(p_file);
	if (ResourceUID::get_singleton()->has_id(uid)) {
		ResourceUID::get_singleton()->set_id(uid, p_file);
	} else {
		ResourceUID::get_singleton()->add_id(uid, p_file);
	}
	
	
	Ref<Resource> r = ResourceCache::get_ref(p_file);
	if (r.is_valid()) {
		if (!r->get_import_path().is_empty()) {
			String dst_path = ResourceFormatImporter::get_singleton()->get_internal_resource_path(p_file);
			r->set_import_path(dst_path);
			r->set_import_last_modified_time(0);
		}
	}
	EditorResourcePreview::get_singleton()->check_for_invalidation(p_file);
	return OK;
}
void EditorFileSystem::_find_group_files(EditorFileSystemDirectory *efd, HashMap<String, Vector<String>> &group_files, HashSet<String> &groups_to_reimport) {