I also vote for same man. Captured serving with the 10th Missouri in July 1863 and sent to POW camps in the North. The objection to being exchanged in 1865 would not have been heeded unless he was allowed to take the oath of allegiance to the USA as a "Confederate deserter" and left the prison. Short of that, he was subject to exchange. There were cases where Confederate prisoners applied to take the oath, but for some reason were declined the privilege. Here's an example, applied to take the oath, but was instead sent back to the Confederacy, and ultimately surrendered and paroled at the close of the war...
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Anyways, the Confederate prisoners from the west, Camp Douglas, were indeed sent to Point Lookout for exchange in early 1865:
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The 10th Missouri was then serving at Shreveport, Louisiana, where it would remain to near the close of the war.
Mr. Whaley was apparently not present with that regiment at the time of surrender.
Instead, he is shown captured at Fort Blakely, April 9, 1865, and recorded with the 1/3rd Missouri Cavalry. Near the close of the war, it was not odd for Confederate soldiers to join units other than those upon which they were mustered. General orders of the Confederate Army had allowed any Confederate foot-soldier who could furnish himself with a suitable mount to be transferred to the cavalry service. [General Order #67, 5-25-1863.]
In the west, many Confederate infantry soldiers didn't bother about official paperwork, but just fell into the cavalry service...
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That said, the 1st and 3rd Cavalry (consolidated) was in fact long already serving as front-line infantry. So it appears more likely, that Mr. Whaley was simply transferred into the 1st & 3rd upon his return to the west by exchange. The regiment, already much reduced number, suffered 60 percent casualties at the Battle of Franklin (Nov. 30, 1864), and participated in the dreadful retreat out of Tennessee and to Tupelo, and then on to Mobile. Missouri Brigade chronicler Ephraim M. Anderson explains that the skeleton command was recruited about Mobile, including a number of exchanged prisoners... and even then, by the Battle of Fort Blakely, the 1st & 3rd regiments consolidated, with their recruits etc. could only physically organize a couple companies (out of 20 represented by the two consolidated regiments!). Ergo if Whaley was an able-bodied Missouri soldier, he was needed to refill the ranks of the skeleton command;
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From p. 399 (and account of the battle of Fort Blakely following)...
As to why the Confederate Army would particularly transfer Whaley of the 10th to the skeletonized 1/3rd Cavalry, it was notable at the time that the 10th was employed in the rear. Where the 1/3rd was still a fighting outfit. And it was noted that the exchanged Confederate prisoners, after their time in the prison camps, were often found in able-bodied condition and so sent right back to the front lines...
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So we next find, from US Prisoner of War records, Whaley as a private of Co. B, 1/3rd MO Cavalry when captured at Fort Blakely, and Recorded as a resident of Washington County, Missouri...
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As a P.O.W. again, he arrived at Ship Island on the Gulf on April 15. He was then sent to Vicksburg, Mississippi on May 1, 1865.
The Prisoners at Ship Island were all sent to Vicksburg and exchanged in early May...
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Ship Island was used as a French base of operations for Gulf Coast maneuvers and later, during the War of 1812, by the British as a launching point for the disastrous Battle of New Orleans. But most memorably, Ship Island served as a Federal prison under the command of Union Major General...
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This was, in fact, just in time for most of them to then be included in the surrender of the Confederate Armies, and, once again as prisoners of war, to receive paroles and allowed to disperse homeward.
His name was shortly after given on the roll of the 1/3rd MO Cav, upon surrender at Citronelle, Alabama in May 13, 1865. He was once again a prisoner of war, but with a parole. The Confederacy, of course, was already crushed out of existence.
However, a last US Military record shows he was among the Confederate prisoners of war classed as "deserters from the Confederate army" and "administered in lieu of the amnesty," at Memphis, Tennessee on June 3, 1865:
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To explain. It might be noted that to the US Army in 1865 a "rebel deserter" was specifically a Confederate soldier who took the oath of allegiance to the United States, and ceased to be a belligerent combatant thereby in the eyes of the USA:
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On May 8, 1865, General Grant ordered that the paroled Confederate soldiers of the surrendered Confederate armies, who desired to return to homes in States outside of those lately in rebellion (like Missouri) could not do so unless they took the oath of allegiance to the United States (that proclaimed Dec. 8, 1863) in order to receive the Presidential amnesty proclaimed most recently in March, 1864. Grant:
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This is a reference to the amnesty proffered by President Lincoln from March 26, 1864, which was offered only to Confederate soldiers who were at large and not in US military custody, but who surrendered themselves for the purpose of taking the oath for the amnesty...
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Such men were given at times as "administered in lieu of the amnesty" (as in taking the oath), or as having "surrendered" their paroles per the S.O. of May 8, 1865 (in order to take the oath and receive the amnesty):
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Anyways, Whaley, after taking the oath at Memphis in June, was free to travel home into Missouri.