If you have not yet posted in Mississippi, you may wish to. Those guys take what could easily be called a "serious approach" to the Civil War having a tendency to knowing the answer to a lot of questions.
As far as desertion go, it is also possible he was laid up somewhere.
I think if they could not find a man or had no idea what had happened, that person was marked down as deserted, My ancestor was listed as deserted and he had gone home to heal after a major battle.
Good luck!