### 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
Ref<DirAccess> da = DirAccess::create(DirAccess::ACCESS_RESOURCES);
		Error ret = da->change_dir(cd);
		ERR_FAIL_COND_MSG(ret != OK, "Cannot change to '" + cd + "' folder.");
		da->list_dir_begin();
		while (true) {
			String f = da->get_next();
			if (f.is_empty()) {
				break;
			}
			if (da->current_is_hidden()) {
				continue;
			}
			if (da->current_is_dir()) {
				if (f.begins_with(".")) { 
					continue;
				}
				int idx = p_dir->find_dir_index(f);
				if (idx == -1) {
					if (_should_skip_directory(cd.path_join(f))) {
						continue;
					}
					EditorFileSystemDirectory *efd = memnew(EditorFileSystemDirectory);
					efd->parent = p_dir;
					efd->name = f;
					Ref<DirAccess> d = DirAccess::create(DirAccess::ACCESS_RESOURCES);
					d->change_dir(cd.path_join(f));
					_scan_new_dir(efd, d, p_progress.get_sub(1, 1));
					ItemAction ia;
					ia.action = ItemAction::ACTION_DIR_ADD;
					ia.dir = p_dir;