### 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)
memdelete(dummy_object);
}
void TileDataCollisionEditor::draw_over_tile(CanvasItem *p_canvas_item, Transform2D p_transform, TileMapCell p_cell, bool p_selected) {
	TileData *tile_data = _get_tile_data(p_cell);
	ERR_FAIL_NULL(tile_data);
	
	Vector<Color> color;
	if (p_selected) {
		Color grid_color = EDITOR_GET("editors/tiles_editor/grid_color");
		Color selection_color = Color().from_hsv(Math::fposmod(grid_color.get_h() + 0.5, 1.0), grid_color.get_s(), grid_color.get_v(), 1.0);
		selection_color.a = 0.7;
		color.push_back(selection_color);
	} else {
		Color debug_collision_color = p_canvas_item->get_tree()->get_debug_collisions_color();
		color.push_back(debug_collision_color);
	}
	RenderingServer::get_singleton()->canvas_item_add_set_transform(p_canvas_item->get_canvas_item(), p_transform);
	Ref<Texture2D> one_way_icon = get_editor_theme_icon(SNAME("OneWayTile"));
	for (int i = 0; i < tile_data->get_collision_polygons_count(physics_layer); i++) {
		Vector<Vector2> polygon = tile_data->get_collision_polygon_points(physics_layer, i);
		if (polygon.size() < 3) {
			continue;
		}
		p_canvas_item->draw_polygon(polygon, color);
		if (tile_data->is_collision_polygon_one_way(physics_layer, i)) {
			PackedVector2Array uvs;
			uvs.resize(polygon.size());