### 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)
}
			layers[0]->set_tile_data(format, p_value);
			emit_signal(CoreStringNames::get_singleton()->changed);
			return true;
		}
		return false;
	} else if (p_name == "cell_quadrant_size") {
		set_rendering_quadrant_size(p_value);
		return true;
	}
#endif 
	else if (components.size() == 2 && components[0].begins_with("layer_") && components[0].trim_prefix("layer_").is_valid_int()) {
		int index = components[0].trim_prefix("layer_").to_int();
		if (index < 0) {
			return false;
		}
		if (index >= (int)layers.size()) {
			while (index >= (int)layers.size()) {
				Ref<TileMapLayer> new_layer;
				new_layer.instantiate();
				new_layer->set_tile_map(this);
				new_layer->set_layer_index_in_tile_map_node(index);
				layers.push_back(new_layer);
			}
			notify_property_list_changed();
			emit_signal(CoreStringNames::get_singleton()->changed);
			update_configuration_warnings();
		}
		if (components[1] == "name") {
			set_layer_name(index, p_value);