### 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)
navigation_map = new_layer_map;
				uses_world_navigation_map = false;
			}
		}
	}
	
	if (forced_cleanup) {
		
		for (KeyValue<Vector2i, CellData> &kv : tile_map) {
			_navigation_clear_cell(kv.value);
		}
	} else {
		if (_navigation_was_cleaned_up || dirty.flags[DIRTY_FLAGS_TILE_MAP_TILE_SET]) {
			
			for (KeyValue<Vector2i, CellData> &kv : tile_map) {
				_navigation_update_cell(kv.value);
			}
		} else {
			
			for (SelfList<CellData> *cell_data_list_element = dirty.cell_list.first(); cell_data_list_element; cell_data_list_element = cell_data_list_element->next()) {
				CellData &cell_data = *cell_data_list_element->self();
				_navigation_update_cell(cell_data);
			}
		}
		if (dirty.flags[DIRTY_FLAGS_TILE_MAP_XFORM]) {
			Transform2D tilemap_xform = tile_map_node->get_global_transform();
			for (KeyValue<Vector2i, CellData> &kv : tile_map) {
				const CellData &cell_data = kv.value;
				
				for (const RID &region : cell_data.navigation_regions) {