### 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)
notify_runtime_tile_data_update(p_layer);
	update_internals();
}
#endif
void TileMap::queue_internal_update() {
	if (pending_update) {
		return;
	}
	pending_update = true;
	callable_mp(this, &TileMap::_internal_update).call_deferred();
}
void TileMap::_internal_update() {
	
	if (!pending_update) {
		return;
	}
	
	
	if (Engine::get_singleton()->is_editor_hint()) {
		polygon_cache.clear();
	}
	
	for (Ref<TileMapLayer> &layer : layers) {
		layer->internal_update();
	}
	pending_update = false;
}
void TileMap::set_tileset(const Ref<TileSet> &p_tileset) {