### 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 (uint32_t i = 0; i < layers.size(); i++) {
		if (layers[i]->has_body_rid(p_physics_body)) {
			return i;
		}
	}
	ERR_FAIL_V_MSG(-1, vformat("No tiles for the given body RID %d.", p_physics_body.get_id()));
}
void TileMap::fix_invalid_tiles() {
	for (Ref<TileMapLayer> &layer : layers) {
		layer->fix_invalid_tiles();
	}
}
void TileMap::clear_layer(int p_layer) {
	TILEMAP_CALL_FOR_LAYER(p_layer, clear)
}
void TileMap::clear() {
	for (Ref<TileMapLayer> &layer : layers) {
		layer->clear();
	}
}
void TileMap::update_internals() {
	pending_update = true;
	_internal_update();
}
void TileMap::notify_runtime_tile_data_update(int p_layer) {