### 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)
for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
									TileSet::CellNeighbor bit = TileSet::CellNeighbor(i);
									array.push_back(tile_data->is_valid_terrain_peering_bit(bit) ? tile_data->get_terrain_peering_bit(bit) : -1);
								}
								dict["terrain_peering_bits"] = array;
								drag_modified[cell] = dict;
								
								tile_data->set_terrain_set(terrain_set);
							}
							drag_last_pos = mb->get_position();
						}
						accept_event();
					} else if (tile_data->get_terrain_set() == terrain_set) {
						
						if (mb->get_button_index() == MouseButton::RIGHT) {
							terrain = -1;
						}
						if (mb->is_command_or_control_pressed() && mb->is_shift_pressed()) {
							
							drag_type = DRAG_TYPE_PAINT_TERRAIN_BITS_RECT;
							drag_modified.clear();
							Dictionary painted_dict;
							painted_dict["terrain_set"] = terrain_set;
							painted_dict["terrain"] = terrain;
							drag_painted_value = painted_dict;
							drag_start_pos = mb->get_position();
						} else {
							
							drag_type = DRAG_TYPE_PAINT_TERRAIN_BITS;
							drag_modified.clear();