### Godot version

v4.0.stable.official [92bee43ad]

### System information

Windows 10, 64bit

### Issue description

First, please run the reproduction project.
When I run the test scene, It report error like follow and app exited. 
![image](https://user-images.githubusercontent.com/35988767/229076194-f737bcb6-6c9b-4aa0-9bd5-3dbd36bc8d03.png)
And I don't know where was error.



### Steps to reproduce

1. Open the reproduction project.
2. Open scene 'user:\\xd\XActors\Weapon\Gun\Rifle\XRifle.tscn'
3. Assign the scene's Meshinstance's mesh with 'user:\\xd\XActors\Weapon\Gun\Rifle\XRifle01.res'
4. Run the scene
Opps, the scene exited.
![GIF](https://user-images.githubusercontent.com/35988767/229077075-4b18b9e0-933e-47f6-b6a8-0af966574884.gif)


### Minimal reproduction project

[GlbTest.zip](https://github.com/godotengine/godot/files/11120181/GlbTest.zip)

NOTE: The project that I provided was picked up from my owner project. Sorry I can't provide a minimal reproduction project because I don't know which step cause this issue. I was test like this:
Create a project, import the glb file, create meshinstance and assign mesh, but there was not error!

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() {
	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]);
		}
	}