Alright, so this idea is to give astrotech beams the ability to repair a ship using a blueprint. You press R on an AstroTech computer, a menu opens, and you insert a blueprint. Connect the astrotech beam to a storage. Behind the scenes, blueprints would have a unique identifier number. When a ship is created using a blueprint, it has the same hidden identifier. When repairing the ship, the beams would replace blocks that are no longer on the ship and repair ones that are damaged, using...
AstroTech Beams - Repair using a blueprint
AstroTech Beams - Repair using a blueprint