### 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)
ERR_FAIL_COND(!p_navigation_mesh.is_valid());
	ERR_FAIL_COND(!p_source_geometry_data.is_valid());
	if (p_navigation_mesh->get_outline_count() == 0 && !p_source_geometry_data->has_data()) {
		p_navigation_mesh->clear();
		if (p_callback.is_valid()) {
			generator_emit_callback(p_callback);
		}
		return;
	}
	baking_navmesh_mutex.lock();
	if (baking_navmeshes.has(p_navigation_mesh)) {
		baking_navmesh_mutex.unlock();
		ERR_FAIL_MSG("NavigationPolygon is already baking. Wait for current bake to finish.");
	}
	baking_navmeshes.insert(p_navigation_mesh);
	baking_navmesh_mutex.unlock();
	generator_bake_from_source_geometry_data(p_navigation_mesh, p_source_geometry_data);
	baking_navmesh_mutex.lock();
	baking_navmeshes.erase(p_navigation_mesh);
	baking_navmesh_mutex.unlock();
	if (p_callback.is_valid()) {
		generator_emit_callback(p_callback);
	}
}
void NavMeshGenerator2D::bake_from_source_geometry_data_async(Ref<NavigationPolygon> p_navigation_mesh, Ref<NavigationMeshSourceGeometryData2D> p_source_geometry_data, const Callable &p_callback) {