I have no further information on John Frank Johnson after his capture and parole. His service record does indicate that he was aboard the Steamer Coatzacoalcos, but does not give a date. That ship was one of three that was used in early August 1862 to move 3,000 CS prisoners from Fort Delaware to the James River for exchange. The Coatzacoalcos departed Fort Delware with 800 prisoners, including such of the invalids as were well enough to leave, on 2 August, arrived at Fort Monroe the same day, and then arrived in the James River on 4 August. The exchange took place at Aiken's Landing on 5 August. There is no evidence, so far, to show John Frank Johnson was exchanged that day. However, based on what I have found about at least one man in the 42nd Va who was a prisoner at Ft. Delaware, at the same time as the transfer, not all the CS prisoners at Ft. Delaware chose to return to CS control. Rather they took the oath of allegiance or joined the Union army. That may have been an option that John Frank Johnson took.
The fact that John Frank Johnson does not show up on the I/48Va muster rolls for May through December 1864 strongly suggests that he had left the army by that time. But the near total lack of records, especially muster rolls, for 1862 and 1863 makes it hard to pinpoint why and when he might have left the service.