### 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_INDEX(polygon[j], navigation_polygon_vertices.size());
								debug_polygon_vertices.write[j] = navigation_polygon_vertices[polygon[j]];
							}
							
							Color random_variation_color = debug_face_color;
							if (enabled_geometry_face_random_color) {
								random_variation_color.set_hsv(
										debug_face_color.get_h() + rand.random(-1.0, 1.0) * 0.1,
										debug_face_color.get_s(),
										debug_face_color.get_v() + rand.random(-1.0, 1.0) * 0.2);
							}
							random_variation_color.a = debug_face_color.a;
							Vector<Color> debug_face_colors;
							debug_face_colors.push_back(random_variation_color);
							rs->canvas_item_add_polygon(p_canvas_item, debug_polygon_vertices, debug_face_colors);
							if (enabled_edge_lines) {
								Vector<Color> debug_edge_colors;
								debug_edge_colors.push_back(debug_edge_color);
								debug_polygon_vertices.push_back(debug_polygon_vertices[0]); 
								rs->canvas_item_add_polyline(p_canvas_item, debug_polygon_vertices, debug_edge_colors);
							}
						}
					}
				}
			}
		}
	}
}
#endif 
void TileMapLayer::_scenes_update() {