Save created child object to empty GameObject in GameBuild ( Not Editor ) - Save to XML?

Ok Guys. What I am trying to do is let the player build a ship with blocks. Got that working ok. The Scene has a EMPTY GameObject called “SHIP” that when you build cubes it adds it to the SHIP as child. So SHIP is always the parent.
In edit It work using PrefabUtility.ReplacePrefab in script. Saving to a prefab and then loading it in the next game scene as the body of the player ship.

The Problem. Game Build fails cause I can’t use PrefabUtility.ReplacePrefab in script.
How can I save one GameObject and it Children objects to xml file. Then Load that XML file to instantiate the object as the ships body.

All the serialization examples I have came across save the scene.

Than you for your Time!

How the Ship create scene looks. it done. cubes gets rebuild via using position. Cube Id and material id. Player can build saves and then used in game