Historical Accuracy, Lincoln's Grand Army, Lincoln's Patriots, Myth of Saving the Union, Northern Resistance to Lincoln 
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The author below records that when Gen. Hooker took command of the Army of the Potomac in late-Jan. 1863, desertions were occurring at a rate of several hundred a day – with about 25 per cent of his assumed strength missing. Senator Henry Wilson stated on the Senate floor in March 1864 that some 40,000 soldiers had already deserted despite executions occurring almost daily in that army.
Northern Desertions, 1863
“Perhaps Lee and the commanders in the South saw with the eyes of the Union scout who wrote from Virginia on November 20, 1862, that desertions form Union lines were so frequent as to be disgusting to Southerners as well.
It is about this time that Lincoln recognized and presented the situation in realistic terms. He pointed out to a group of women calling upon him that while Gen. McClellan was constantly calling for more and more troops, that deserters and furloughed men outnumbered the new recruits; and that while that general had 180,000 men on the rolls for the Antietam battle, he had had only some 90,000 with which to enter the fight, as 20,000 men were in hospitals and the rest “absent,” and that within two hours after the battle, some 30,000 had straggled and deserted.
Northern General Pope in September of that year had reported the straggling as so bad that unless something were done to restore tone to the army, it would “melt away before you know it.”
No less a figure than Gen. Halleck charged that not a few Northern soldiers voluntarily surrendered to the enemy in order to be paroled as prisoners of war. Even the vigilance of escorts and guards was materially affected by the alluring thought that captivity meant liberty and relaxation. Many Northern soldiers, according to Generals Meade and McClellan, dispersed and left during the Antietam battle.
Every Northern defeat was marked by a long line of stragglers and deserters, who, if the outcome had been different, would probably have remained to press on the advantage. And the number absent without leave in late December 1862, after Gen. Burnside’s disaster at Fredericksburg, worsened the losses and the demoralization of Lincoln’s army was complete.”
(Desertions During the Civil War. Ella Lonn. University of Nebraska Press, 1998, pg. 144-145. (original American Historical Association, 1928)