### 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)
Ref<InputEventMouseMotion> mm = p_event;
	if (mm.is_valid()) {
		if (drag_type == DRAG_TYPE_PAINT_TERRAIN_SET) {
			Vector<Vector2i> line = Geometry2D::bresenham_line(p_tile_atlas_view->get_atlas_tile_coords_at_pos(drag_last_pos, true), p_tile_atlas_view->get_atlas_tile_coords_at_pos(mm->get_position(), true));
			for (int i = 0; i < line.size(); i++) {
				Vector2i coords = p_tile_set_atlas_source->get_tile_at_coords(line[i]);
				if (coords != TileSetSource::INVALID_ATLAS_COORDS) {
					int terrain_set = drag_painted_value;
					TileMapCell cell;
					cell.source_id = 0;
					cell.set_atlas_coords(coords);
					cell.alternative_tile = 0;
					
					TileData *tile_data = p_tile_set_atlas_source->get_tile_data(coords, 0);
					if (!drag_modified.has(cell)) {
						Dictionary dict;
						dict["terrain_set"] = tile_data->get_terrain_set();
						dict["terrain"] = tile_data->get_terrain();
						Array array;
						for (int j = 0; j < TileSet::CELL_NEIGHBOR_MAX; j++) {
							TileSet::CellNeighbor bit = TileSet::CellNeighbor(j);
							array.push_back(tile_data->is_valid_terrain_peering_bit(bit) ? tile_data->get_terrain_peering_bit(bit) : -1);
						}
						dict["terrain_peering_bits"] = array;
						drag_modified[cell] = dict;
					}
					
					tile_data->set_terrain_set(terrain_set);