### 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)
tile_data->set_z_index(ctd->autotile_z_index_map[coords]);
							}
							
							if (ctd->shapes.size() > 0) {
								if (get_physics_layers_count() < 1) {
									add_physics_layer();
								}
							}
							for (int k = 0; k < ctd->shapes.size(); k++) {
								CompatibilityShapeData csd = ctd->shapes[k];
								if (csd.autotile_coords == coords) {
									Ref<ConvexPolygonShape2D> convex_shape = csd.shape; 
									if (convex_shape.is_valid()) {
										Vector<Vector2> polygon = convex_shape->get_points();
										for (int point_index = 0; point_index < polygon.size(); point_index++) {
											polygon.write[point_index] = xform.xform(csd.transform.xform(polygon[point_index]) - ctd->autotile_tile_size / 2.0);
										}
										tile_data->set_collision_polygons_count(0, tile_data->get_collision_polygons_count(0) + 1);
										int index = tile_data->get_collision_polygons_count(0) - 1;
										tile_data->set_collision_polygon_one_way(0, index, csd.one_way);
										tile_data->set_collision_polygon_one_way_margin(0, index, csd.one_way_margin);
										tile_data->set_collision_polygon_points(0, index, polygon);
									}
								}
							}