### 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)
if (!region.is_valid()) {
						continue;
					}
					Transform2D tile_transform;
					tile_transform.set_origin(tile_map_node->map_to_local(kv.key));
					NavigationServer2D::get_singleton()->region_set_transform(region, tilemap_xform * tile_transform);
				}
			}
		}
	}
	
	
	_navigation_was_cleaned_up = forced_cleanup;
}
void TileMapLayer::_navigation_clear_cell(CellData &r_cell_data) {
	NavigationServer2D *ns = NavigationServer2D::get_singleton();
	
	for (uint32_t i = 0; i < r_cell_data.navigation_regions.size(); i++) {
		const RID &region = r_cell_data.navigation_regions[i];
		if (region.is_valid()) {
			ns->region_set_map(region, RID());
			ns->free(region);
		}
	}
	r_cell_data.navigation_regions.clear();
}
void TileMapLayer::_navigation_update_cell(CellData &r_cell_data) {
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	NavigationServer2D *ns = NavigationServer2D::get_singleton();
	Transform2D tilemap_xform = tile_map_node->get_global_transform();