I don’t remember any part of the check in process where I would have been able to put the case back in with the rest of my luggage.

That’s odd. I’ve flown with a pistol several times and it’s always been the other way around. After TSA does their check the locked pistol case gets put back inside a piece of my checked luggage. What have they done with yours? Just tossed it on the conveyor belt like its another piece of luggage?