### 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)
ERR_FAIL_NULL(NavigationServer2D::get_singleton());
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	NavigationServer2D *ns = NavigationServer2D::get_singleton();
	
	bool forced_cleanup = in_destructor || !enabled || !navigation_enabled || !tile_map_node->is_inside_tree() || !tile_set.is_valid();
	
	if (forced_cleanup) {
		if (navigation_map.is_valid() && !uses_world_navigation_map) {
			ns->free(navigation_map);
			navigation_map = RID();
		}
	} else {
		
		if (!navigation_map.is_valid()) {
			if (layer_index_in_tile_map_node == 0) {
				
				navigation_map = tile_map_node->get_world_2d()->get_navigation_map();
				uses_world_navigation_map = true;
			} else {
				RID new_layer_map = ns->map_create();
				
				ns->map_set_cell_size(new_layer_map, 1.0);
				ns->map_set_active(new_layer_map, true);