As an update to this situation: I decided to upgrade my brother-in-law from C to F on NRT-LAX last week. When I put in for the upgrade on United.bomb, it said I had a SWU reserved, but didn't pull one from my available balance. When he flew, the balance stayed at 2 SWUs, but the usage showed that a SWU was pulled and used for the upgrade. It seems that there is a never land in between what United.bomb shows as your upgrade balance and what the balance really is. It looks like this resolved my problem.