I'm a little out of my specialty on this, but if the highest Union authorities ordered a halt to "all paroles for Confederates from Missouri and Kentucky" and the date is correct as 11 May 1865, the reason may be strictly a legal one. You DO mean 1865?

What bothers me is that the War Dept. sent this order to Vicksburg, which in May 1865 had been under solid Union control for almost two years at that time. Perhaps Confederates were coming in to Vicksburg to surrender, and officials in Washington wanted to ensure that surrenders were final. Paroles in some circumstances are not permanent, and paroled combatants can resume warfare under certain conditions. In May 1865 the concern of the Union military in the Trans-Mississippi West was the orderly surrender of all remaining Confederate forces, mostly in Arkansas, Louisiana, and Texas. As I understand it, Federal authorities insisted on surrender and nothing less from any and all remaining Confederate military groups, preferably voluntary.

Now, back to the Missouri and Kentucky part of the equation. I am a bit foggy on the Kentucky part, but I know that U.S. authorities never recognized that Missouri seceded, never considered Missouri as an occupied belligerent state. The proof of this unique status is that Lincoln's Emancipation Proclamation in autumn 1862 never applied to Missouri. The Missouri General Assembly finally enacted its own emancipation of slaves effective 11 January 1865 for the few slaves still remaining in the state by that date. In other words, Federal authorities steadfastly refused to consider Missouri legally as anything else than a part of the Union through the entire war. There was little occupation of Missouri under Reconstruction by Union troops for any reason except to restore civil law, which had to be enforced to counter lawlessness and anarchy that resulted from four-and-one-half years of continuous guerrilla war. I would guess that Kentucky was treated much the same by Federal authorities as a fellow border state, but I really do not know about Kentucky. Because of Missouri's special treatment by Federal authorities and the great number of southern adherents living there, the order not to take paroles may stem from U.S. concerns that southern combatants may wish to continue the war on home ground in the future, but my suggestion of this is strictly conjecture.

My strongest suggestion why Union leaders were directed not to take paroles is they are not final whereas surrender, depending on the conditions agreed to by both parties at the surrender, are final.

That being said, my Law of Modern Warfare instruction was many years ago, and if any part of the above is wrong, please point it out to me.

Bruce Nichols