### 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)
bool show_navigation = false;
	switch (tile_map_node->get_navigation_visibility_mode()) {
		case TileMap::VISIBILITY_MODE_DEFAULT:
			show_navigation = !Engine::get_singleton()->is_editor_hint() && tile_map_node->get_tree()->is_debugging_navigation_hint();
			break;
		case TileMap::VISIBILITY_MODE_FORCE_HIDE:
			show_navigation = false;
			break;
		case TileMap::VISIBILITY_MODE_FORCE_SHOW:
			show_navigation = true;
			break;
	}
	if (!show_navigation) {
		return;
	}
	
	if (r_cell_data.navigation_regions.is_empty()) {
		return;
	}
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	RenderingServer *rs = RenderingServer::get_singleton();
	const NavigationServer2D *ns2d = NavigationServer2D::get_singleton();
	bool enabled_geometry_face_random_color = ns2d->get_debug_navigation_enable_geometry_face_random_color();
	bool enabled_edge_lines = ns2d->get_debug_navigation_enable_edge_lines();
	Color debug_face_color = ns2d->get_debug_navigation_geometry_face_color();
	Color debug_edge_color = ns2d->get_debug_navigation_geometry_edge_color();
	RandomPCG rand;