### 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 node_visible = tile_map_node->is_visible_in_tree();
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	RenderingServer *rs = RenderingServer::get_singleton();
	
	for (uint32_t i = tile_set->get_occlusion_layers_count(); i < r_cell_data.occluders.size(); i++) {
		RID occluder_id = r_cell_data.occluders[i];
		if (occluder_id.is_valid()) {
			rs->free(occluder_id);
		}
	}
	r_cell_data.occluders.resize(tile_set->get_occlusion_layers_count());
	TileSetSource *source;
	if (tile_set->has_source(r_cell_data.cell.source_id)) {
		source = *tile_set->get_source(r_cell_data.cell.source_id);
		if (source->has_tile(r_cell_data.cell.get_atlas_coords()) && source->has_alternative_tile(r_cell_data.cell.get_atlas_coords(), r_cell_data.cell.alternative_tile)) {
			TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
			if (atlas_source) {
				
				const TileData *tile_data;
				if (r_cell_data.runtime_tile_data_cache) {
					tile_data = r_cell_data.runtime_tile_data_cache;
				} else {
					tile_data = atlas_source->get_tile_data(r_cell_data.cell.get_atlas_coords(), r_cell_data.cell.alternative_tile);
				}
				
				for (uint32_t occlusion_layer_index = 0; occlusion_layer_index < r_cell_data.occluders.size(); occlusion_layer_index++) {
					Ref<OccluderPolygon2D> occluder_polygon = tile_data->get_occluder(occlusion_layer_index);