Correct. The 104k deserter number is based on the "fragmentary" and "defective" Confederate records secured after the war in the hands of the War Department/National Archives...
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There were no Confederate "muster out" rolls, so it is impossible to know the total number of casualties in any given unit. It seems to have been understood that AWOL's were so common, that the officers were frequently loath to report men as deserters unless pressed to do so.
In response to an inquiry in August, 1869, late-Confederate Adjutant General Samuel Cooper stated the monthly returns for the Army, per his recollection, in the last two years of the war, informed him the CS Army never hand on hand more than just over half of the men on the rolls at any one time...
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Col. Robert G.H. Kean, Chief of the Bureau of War in Richmond, complained by mid-1863 that Cooper's office had failed to compel any of the forces to produce these returns with accuracy and completeness...
"....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."
Cooper, for example, admitted in an 1864 notice, that he had no means of compiling data on the recruits and conscripts, etc. Total Confederate casualties of all kinds, including wartime desertion, are consequently unknown. And according to Dr. Jones of the CS Medical Department, unknowable, with no way to determine the total had even the Confederacy succeeded...
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