### 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)
return group_file_cache.has(p_path);
}
void EditorFileSystem::_move_group_files(EditorFileSystemDirectory *efd, const String &p_group_file, const String &p_new_location) {
	int fc = efd->files.size();
	EditorFileSystemDirectory::FileInfo *const *files = efd->files.ptrw();
	for (int i = 0; i < fc; i++) {
		if (files[i]->import_group_file == p_group_file) {
			files[i]->import_group_file = p_new_location;
			Ref<ConfigFile> config;
			config.instantiate();
			String path = efd->get_file_path(i) + ".import";
			Error err = config->load(path);
			if (err != OK) {
				continue;