My second thought after my first happy thought of the homeowner defending his life and home was, did the police swipe EVERY gun he had in his collection for "evidence"?
Every class that I have had that touched on this topic said no.
They will take the weapon(s) used. The others have nothing to do with the case. I guess that if you showed outward signs that you were going to go on a vengeance shooting spree they might look into it. Otherwise I think you would be safe. Just don't load up while they are doing the initial investigation.
That's why you have multiples of the same firearm. No need to retrain yourself in how they work.