### Godot version

v4.1.beta.custom_build [72b59325c]

### System information

Windows 10, Vulkan

### Issue description

This has been plaguing me for a while in my main project. I can only partially reproduce it in a MRP:
When placing a binary mesh resource imported from a .glb file into a MeshInstance3D, it will be gone upon restart. It doesn't seem to happen to every resource, but I've had MIs that were fine and then start doing it out of nowhere.
I thought it was going to be related to materials due to things like https://github.com/godotengine/godot/issues/77007 but I can reliably trigger it with the steps listed below.
I have done limited testing on .tres files because I usually use .res for size/performance, but in the MRP .tres doesn't seem to trigger it, so perhaps it doesn't affect those.

Note on the Steps to reproduce: you have to delete the test_cube.res and redo the steps to trigger the bug again, but in my main project the affected resources always disappear.

### Steps to reproduce

1. Double click test_cube.glb
2. Click the mesh (test_cube_Cube_097), set save to file path as: res://test_cube.res
3. Make sure to click the little folder icon and then Save (this seems to make it consistent to proc)
4. Press Reimport
5. Drag the test_cube.res to the Mesh slot of the MeshInstance3D
6. Ctrl+s to save
7. Project -> Reload current project
8. Mesh is no longer in the MeshInstance3D

### Minimal reproduction project

[binary res bug.zip](https://github.com/godotengine/godot/files/11681009/binary.res.bug.zip)
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]);
		}
	}