Okay OOO, this is very simple. When you finish a Shadow Lair, you should get everything as normal. However, a machine in Haven could be added that requires you have a lair's reward rarity module thing and that lets you craft the lair's items. This way it won't effect the keys as people will still need to go to lairs for materials, but it'll let people who have spare SL boss items make something out of them.