### 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)
update_script_mutex.lock();
	update_script_paths.insert(p_path);
	update_script_mutex.unlock();
}
void EditorFileSystem::update_file(const String &p_file) {
	ERR_FAIL_COND(p_file.is_empty());
	EditorFileSystemDirectory *fs = nullptr;
	int cpos = -1;
	if (!_find_file(p_file, &fs, cpos)) {
		if (!fs) {
			return;
		}
	}
	if (!FileAccess::exists(p_file)) {
		
		_delete_internal_files(p_file);
		if (cpos != -1) { 
			if (fs->files[cpos]->uid != ResourceUID::INVALID_ID) {
				if (ResourceUID::get_singleton()->has_id(fs->files[cpos]->uid)) {
					ResourceUID::get_singleton()->remove_id(fs->files[cpos]->uid);
				}
			}
			if (ClassDB::is_parent_class(fs->files[cpos]->type, SNAME("Script"))) {
				_queue_update_script_class(p_file);
			}
			memdelete(fs->files[cpos]);
			fs->files.remove_at(cpos);
		}
		_update_pending_script_classes();