Early 11/1864 Brother, George, reported that Allen was conscripted into the Confederate forces under Gen Price as the two were making molasses. Whether Allen went willingly or not is unknown.
Shortly after he was back, either on a mission or as a deserter. George later alleged that Allen and a man named Fagin were trying to surrender to Union forces at Fagin's house when a group of Federal forces surprized them and during the mayhem, Allen was shot. Apparently the wound was not fatal as evidenced by the next item.