### 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)
Vector<Vector2> polypath;
		for (const Point64 &scaled_point : scaled_path) {
			polypath.push_back(Vector2(static_cast<real_t>(scaled_point.x), static_cast<real_t>(scaled_point.y)));
		}
		new_baked_outlines.push_back(polypath);
	}
	if (new_baked_outlines.size() == 0) {
		p_navigation_mesh->set_vertices(Vector<Vector2>());
		p_navigation_mesh->clear_polygons();
		return;
	}
	Paths64 polygon_paths;
	for (const Vector<Vector2> &baked_outline : new_baked_outlines) {
		Path64 polygon_path;
		for (const Vector2 &baked_outline_point : baked_outline) {
			const Point64 &point = Point64(baked_outline_point.x, baked_outline_point.y);
			polygon_path.push_back(point);
		}
		polygon_paths.push_back(polygon_path);
	}
	ClipType clipper_cliptype = ClipType::Union;
	List<TPPLPoly> tppl_in_polygon, tppl_out_polygon;
	PolyTree64 polytree;
	Clipper64 clipper_64;
	clipper_64.AddSubject(polygon_paths);
	clipper_64.Execute(clipper_cliptype, FillRule::NonZero, polytree);
	for (size_t i = 0; i < polytree.Count(); i++) {
		const PolyPath64 *polypath_item = polytree[i];
		generator_recursive_process_polytree_items(tppl_in_polygon, polypath_item);
	}