### 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_V(p_layer_id, physics.size(), 0);
	ERR_FAIL_INDEX_V(p_polygon_index, physics[p_layer_id].polygons.size(), 0);
	return physics[p_layer_id].polygons[p_polygon_index].shapes.size();
}
Ref<ConvexPolygonShape2D> TileData::get_collision_polygon_shape(int p_layer_id, int p_polygon_index, int shape_index) const {
	ERR_FAIL_INDEX_V(p_layer_id, physics.size(), Ref<ConvexPolygonShape2D>());
	ERR_FAIL_INDEX_V(p_polygon_index, physics[p_layer_id].polygons.size(), Ref<ConvexPolygonShape2D>());
	ERR_FAIL_INDEX_V(shape_index, (int)physics[p_layer_id].polygons[p_polygon_index].shapes.size(), Ref<ConvexPolygonShape2D>());
	return physics[p_layer_id].polygons[p_polygon_index].shapes[shape_index];
}
void TileData::set_terrain_set(int p_terrain_set) {
	ERR_FAIL_COND(p_terrain_set < -1);
	if (p_terrain_set == terrain_set) {
		return;
	}
	if (tile_set) {
		ERR_FAIL_COND(p_terrain_set >= tile_set->get_terrain_sets_count());
		terrain = -1;
		for (int i = 0; i < 16; i++) {
			terrain_peering_bits[i] = -1;
		}
	}
	terrain_set = p_terrain_set;
	notify_property_list_changed();
	emit_signal(SNAME("changed"));
}
int TileData::get_terrain_set() const {