### 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)
TileData *tile_data = p_tile_set_atlas_source->get_tile_data(p_coords, p_alternative_tile);
	ERR_FAIL_NULL_V(tile_data, Variant());
	Dictionary dict;
	dict["linear_velocity"] = tile_data->get_constant_linear_velocity(physics_layer);
	dict["angular_velocity"] = tile_data->get_constant_angular_velocity(physics_layer);
	Array array;
	for (int i = 0; i < tile_data->get_collision_polygons_count(physics_layer); i++) {
		Dictionary polygon_dict;
		polygon_dict["points"] = tile_data->get_collision_polygon_points(physics_layer, i);
		polygon_dict["one_way"] = tile_data->is_collision_polygon_one_way(physics_layer, i);
		polygon_dict["one_way_margin"] = tile_data->get_collision_polygon_one_way_margin(physics_layer, i);
		array.push_back(polygon_dict);
	}
	dict["polygons"] = array;
	return dict;
}
void TileDataCollisionEditor::_setup_undo_redo_action(TileSetAtlasSource *p_tile_set_atlas_source, HashMap<TileMapCell, Variant, TileMapCell> p_previous_values, Variant p_new_value) {