### 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
int fc = d->get_file_count();
	for (int i = 0; i < fc; i++) {
		if (d->get_file_type(i) == SNAME("GDExtension")) {
			extensions.insert(d->get_file_path(i));
		}
	}
	int dc = d->get_subdir_count();
	for (int i = 0; i < dc; i++) {
		_scan_extensions_dir(d->get_subdir(i), extensions);
	}
}
bool EditorFileSystem::_scan_extensions() {