### 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)
}
						terrain_set_property_editor->update_property();
						_update_terrain_selector();
						picker_button->set_pressed(false);
						accept_event();
					}
				} else {
					int terrain_set = int(dummy_object->get("terrain_set"));
					int terrain = int(dummy_object->get("terrain"));
					Vector3i tile = p_tile_atlas_view->get_alternative_tile_at_pos(mb->get_position());
					Vector2i coords = Vector2i(tile.x, tile.y);
					int alternative_tile = tile.z;
					if (coords != TileSetSource::INVALID_ATLAS_COORDS) {
						TileData *tile_data = p_tile_set_atlas_source->get_tile_data(coords, alternative_tile);
						if (terrain_set == -1 || !tile_data || tile_data->get_terrain_set() != terrain_set) {
							
							drag_type = DRAG_TYPE_PAINT_TERRAIN_SET;
							drag_modified.clear();
							drag_painted_value = int(dummy_object->get("terrain_set"));
							if (coords != TileSetSource::INVALID_ATLAS_COORDS) {
								TileMapCell cell;
								cell.source_id = 0;
								cell.set_atlas_coords(coords);
								cell.alternative_tile = alternative_tile;
								Dictionary dict;
								dict["terrain_set"] = tile_data->get_terrain_set();
								Array array;
								for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
									TileSet::CellNeighbor bit = TileSet::CellNeighbor(i);
									array.push_back(tile_data->is_valid_terrain_peering_bit(bit) ? tile_data->get_terrain_peering_bit(bit) : -1);