### 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 (navigation_polygon.is_valid() && (navigation_polygon->get_polygon_count() > 0 || navigation_polygon->get_outline_count() > 0)) {
						
						Transform2D tile_transform;
						tile_transform.set_origin(tile_map_node->map_to_local(r_cell_data.coords));
						if (!region.is_valid()) {
							region = ns->region_create();
						}
						ns->region_set_owner_id(region, tile_map_node->get_instance_id());
						ns->region_set_map(region, navigation_map);
						ns->region_set_transform(region, tilemap_xform * tile_transform);
						ns->region_set_navigation_layers(region, tile_set->get_navigation_layer_layers(navigation_layer_index));
						ns->region_set_navigation_polygon(region, navigation_polygon);
					} else {
						
						if (region.is_valid()) {
							ns->region_set_map(region, RID());
							ns->free(region);
							region = RID();
						}
					}
				}
				return;
			}
		}
	}
	
	_navigation_clear_cell(r_cell_data);
}
#ifdef DEBUG_ENABLED
void TileMapLayer::_navigation_draw_cell_debug(const RID &p_canvas_item, const Vector2i &p_quadrant_pos, const CellData &r_cell_data) {