### 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)
late_update_files.insert(p_file);
		_save_late_updated_files(); 
	}
	fs->files[cpos]->type = type;
	fs->files[cpos]->resource_script_class = script_class;
	fs->files[cpos]->uid = uid;
	fs->files[cpos]->script_class_name = _get_global_script_class(type, p_file, &fs->files[cpos]->script_class_extends, &fs->files[cpos]->script_class_icon_path);
	fs->files[cpos]->import_group_file = ResourceLoader::get_import_group_file(p_file);
	fs->files[cpos]->modified_time = FileAccess::get_modified_time(p_file);
	fs->files[cpos]->deps = _get_dependencies(p_file);
	fs->files[cpos]->import_valid = type == "TextFile" ? true : ResourceLoader::is_import_valid(p_file);
	if (uid != ResourceUID::INVALID_ID) {
		if (ResourceUID::get_singleton()->has_id(uid)) {
			ResourceUID::get_singleton()->set_id(uid, p_file);
		} else {
			ResourceUID::get_singleton()->add_id(uid, p_file);
		}
		ResourceUID::get_singleton()->update_cache();
	}
	
	EditorResourcePreview::get_singleton()->check_for_invalidation(p_file);
	if (ClassDB::is_parent_class(fs->files[cpos]->type, SNAME("Script"))) {
		_queue_update_script_class(p_file);
	}
	_update_pending_script_classes();
	call_deferred(SNAME("emit_signal"), "filesystem_changed"); 
}
HashSet<String> EditorFileSystem::get_valid_extensions() const {