I agree with Res Dog that you will more than likely be ok.
6 or 7 yrs ago when built my first sbr, they wouldn't let me list multiple calibers. I had a 11 inch 5.56 and a 10 inch tros 9mm upper. Was told to register one and write a letter stating that I would occationally use the 10 inch 9mm barrel on registered sbr lower. I carry a copy with form 1 copy. Since I had multiple AR's laying around and stripped lowers, I was advised to have lowers on hand registered as pistols to maintain legality for other short uppesr on site. This is probably overkill, but I got a couple cheap blemed lowers logged out as handguns and stamped them pistol only. So basicly they are stripped lowers with take down pins. Only cost me $45 each. You could also get ya a couple 10 dollar forgings and drill the take down pins as close as you can and stamp pistol only with some serial number. They don't have to be functional.