Christy - One document in the pension application will be a summary of his service from the War Department from the documents now in the National Archives. If this document had any indcation of desertion or dropped from the rolls, the pension would not have been approved. I suspect that your ancestor was commissioned to command a group of returned deserters, and not that he was a deserter himself. I know of no case where the Confederacy would have granted a commission to any such person.