### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
cleanup();
}
void NavMeshGenerator2D::sync() {
	if (generator_tasks.size() == 0) {
		return;
	}
	baking_navmesh_mutex.lock();
	generator_task_mutex.lock();
	LocalVector<WorkerThreadPool::TaskID> finished_task_ids;
	for (KeyValue<WorkerThreadPool::TaskID, NavMeshGeneratorTask2D *> &E : generator_tasks) {
		if (WorkerThreadPool::get_singleton()->is_task_completed(E.key)) {
			WorkerThreadPool::get_singleton()->wait_for_task_completion(E.key);
			finished_task_ids.push_back(E.key);
			NavMeshGeneratorTask2D *generator_task = E.value;
			DEV_ASSERT(generator_task->status == NavMeshGeneratorTask2D::TaskStatus::BAKING_FINISHED);
			baking_navmeshes.erase(generator_task->navigation_mesh);
			if (generator_task->callback.is_valid()) {
				generator_emit_callback(generator_task->callback);
			}
			memdelete(generator_task);
		}
	}
	for (WorkerThreadPool::TaskID finished_task_id : finished_task_ids) {
		generator_tasks.erase(finished_task_id);
	}
	generator_task_mutex.unlock();
	baking_navmesh_mutex.unlock();
}
void NavMeshGenerator2D::cleanup() {