### 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
EditorFileSystemDirectory *d = get_filesystem();
	HashSet<String> extensions;
	_scan_extensions_dir(d, extensions);
	
	Vector<String> extensions_added;
	Vector<String> extensions_removed;
	for (const String &E : extensions) {
		if (!GDExtensionManager::get_singleton()->is_extension_loaded(E)) {
			extensions_added.push_back(E);
		}
	}
	Vector<String> loaded_extensions = GDExtensionManager::get_singleton()->get_loaded_extensions();
	for (int i = 0; i < loaded_extensions.size(); i++) {
		if (!extensions.has(loaded_extensions[i])) {
			extensions_removed.push_back(loaded_extensions[i]);
		}
	}
	String extension_list_config_file = GDExtension::get_extension_list_config_file();
	if (extensions.size()) {
		if (extensions_added.size() || extensions_removed.size()) { 
			Ref<FileAccess> f = FileAccess::open(extension_list_config_file, FileAccess::WRITE);