### 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
ERR_FAIL_INDEX_V(p_idx, subdirs.size(), nullptr);
	return subdirs[p_idx];
}
int EditorFileSystemDirectory::get_file_count() const {
	return files.size();
}
String EditorFileSystemDirectory::get_file(int p_idx) const {
	ERR_FAIL_INDEX_V(p_idx, files.size(), "");
	return files[p_idx]->file;
}
String EditorFileSystemDirectory::get_path() const {
	String p;
	const EditorFileSystemDirectory *d = this;
	while (d->parent) {
		p = d->name.path_join(p);
		d = d->parent;
	}
	return "res://" + p;
}
String EditorFileSystemDirectory::get_file_path(int p_idx) const {
	String file = get_file(p_idx);
	const EditorFileSystemDirectory *d = this;
	while (d->parent) {
		file = d->name.path_join(file);
		d = d->parent;
	}
	return "res://" + file;
}
Vector<String> EditorFileSystemDirectory::get_file_deps(int p_idx) const {