### 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)
TPPLPartition tpart;
	if (tpart.ConvexPartition_HM(&tppl_in_polygon, &tppl_out_polygon) == 0) { 
		ERR_PRINT("NavigationPolygon Convex partition failed. Unable to create a valid NavigationMesh from defined polygon outline paths.");
		p_navigation_mesh->set_vertices(Vector<Vector2>());
		p_navigation_mesh->clear_polygons();
		return;
	}
	Vector<Vector2> new_vertices;
	Vector<Vector<int>> new_polygons;
	HashMap<Vector2, int> points;
	for (List<TPPLPoly>::Element *I = tppl_out_polygon.front(); I; I = I->next()) {
		TPPLPoly &tp = I->get();
		Vector<int> new_polygon;
		for (int64_t i = 0; i < tp.GetNumPoints(); i++) {
			HashMap<Vector2, int>::Iterator E = points.find(tp[i]);
			if (!E) {
				E = points.insert(tp[i], new_vertices.size());
				new_vertices.push_back(tp[i]);
			}
			new_polygon.push_back(E->value);
		}
		new_polygons.push_back(new_polygon);
	}
	p_navigation_mesh->set_vertices(new_vertices);
	p_navigation_mesh->clear_polygons();
	for (int i = 0; i < new_polygons.size(); i++) {
		p_navigation_mesh->add_polygon(new_polygons[i]);
	}
}