### 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)
}
			if (config->has_section_key("remap", "group_file")) {
				config->set_value("remap", "group_file", p_new_location);
			}
			List<String> sk;
			config->get_section_keys("params", &sk);
			for (const String &param : sk) {
				
				String value = config->get_value("params", param);
				if (value == p_group_file) {
					config->set_value("params", param, p_new_location);
				}
			}
			config->save(path);
		}
	}
	for (int i = 0; i < efd->get_subdir_count(); i++) {
		_move_group_files(efd->get_subdir(i), p_group_file, p_new_location);
	}
}
void EditorFileSystem::move_group_file(const String &p_path, const String &p_new_path) {
	if (get_filesystem()) {
		_move_group_files(get_filesystem(), p_path, p_new_path);
		if (group_file_cache.has(p_path)) {
			group_file_cache.erase(p_path);
			group_file_cache.insert(p_new_path);
		}
	}
}
ResourceUID::ID EditorFileSystem::_resource_saver_get_resource_id_for_path(const String &p_path, bool p_generate) {