I am inclined to think that he was never there. From the Provost Marshal's Files for Individuals, I have a copy of a personal letter written by Governor Gamble on his behalf requesting that the assessment under Halleck's General Order 24 be reconsidered in his case. RMR had face-face experience with many of the key players on both sides at a pretty high level.
While that is before the time of this reported arrest, it is an accurate statement of affairs at that early time. At the time of this reported arrest/incarceration, the same PMF source is of RMR's request for extension of the bounds of his existing parole to allow his attendance at the Democratic Convention originally planned for May, 1864, but then moved to August. Since he was an elected delegate, his request to go to Chicago was approved.
You or others probably already have most of Ms. Eakin's books. When mine arrive, I'll gladly share what I learn.
Thanks again.