I try to read all your posts, so I've had time to mull over your thoughts about this man and his situation. The Confederates evacuated some of the wounded before Fort Donelson surrendered, so it's possible Vandiver's wound was the result of hostile action. It's almost as likely that the injury occured as you described, an accidental shooting while on picket, in camp or even while on leave.

The best example of a Confederate officer who continued in service after loss of an arm or leg is General John B. Hood, in his case one of each. I can't recall another case in which an enlisted man remained in service after loss of an arm or leg, or was elected a company officer. Rather than attempting to describe specific physical limitations, the law allowed qualified medical officers to determine whether or not a man could render any useful military service to his country. That's the part we don't know for sure.

It appears that this man went home on leave, didn't return for one reason or another, and was picked up at or near home by the Yankees. Desertion from Confederate ranks increased after the surrender of Vicksburg, and hundreds of soldiers from northwest Mississippi went to prison as deserters. Apparently Federal authorities decided not to send this crippled soldier north, so he was released on oath of allegiance (my best guess as to what happened next).

There's more going on with Vandiver than we can appreciate from the available records - we just don't have all the facts.