I speculate that "Old Abner's shoes" refers to the narrator of the song: an infantryman belonging to Abner's command (hence "Abner's shoes") who was stolen (i.e., captured) by the Yankees.
Treating Abner as the narrator of the song contradicts the verse that says that Abner was not there when the Yankees arrived. If the narrator was not there, then how could he become a prisoner?