Archivist Henry P. Beers in his review of Confederate records, found none from the prison at Millen...
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I haven't seen any evidence to suggest the Confederate military prison authorities were any more thorough or efficient than in the Confederate Army generally (on the contrary perhaps). Records and returns were incomplete. Col. Robert G.H. Kean, Chief of the Bureau of War in Richmond, complained that the Army's adjutant general's office, under General Cooper, by mid-1863 had failed to compel any of the forces to produce complete returns.
"....one would suppose that the office highest in rank, the official keeper of the rolls whose specific duty it to know the state of the army and compel proper returns, would in two and a half years have got some complete returns. Yet it is notorious that the returns are not complete even from the nearest and most stationary army, while of the Trans-Mississippi forces, they have almost no account whatever. There has never been a time when the A.I. General could give even a tolerably close guess of the whole force on the rolls of the army, still less of the effective force."
Consequently, if that was the status of their own forces, it should perhaps not be surprising their record of POW's was equally incomplete.
Dr. Joseph Jones of the CS Army Medical department, during the war, toured many of the larger military hospitals and even the prisons, for data on medical conditions and mortality. This included a report about the circumstances at Andersonville, which he claimed US forces after the war confiscated from him...
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Given the subsequent military trial and execution of Captain Wirz, I would imagine, rendered it unlikely any Southern officers who retained prison records, including record of the deceased, were inclined to come forward with them.