At the time, Vaughn was in command of Confederate troops in East Tennessee commanding an assortment of troops. The bulk of Vaughn’s Cavalry Brigade, formed back in November, 1863, was still with Early in the Shenandoah Valley at the time (shortly to arrive back in East Tennessee) although he had been invalided back to East Tennessee sometime earlier.

HDQRS. DEPT. OF W. VA. AND E. TENN.,
Carter's Station, September 5, 1864.
I. Col. George B. Crittenden is relieved from the command of the troops in East Tennessee and Brig. Gen. John C. Vaughn is assigned to the command of the same.
II. Brig. Gen. G. B. Cosby having reported for duty, under assignment from the War Department to the brigade formerly commanded by Brigadier-General Hodge, will at once assume command of said brigade.
III. Col. George B. Crittenden is assigned to duty as inspector-general of the troops now in East Tennessee, and will at once enter upon the discharge of his duties.
IV. Col. D. Howard Smith is relieved from the command of the brigade composed of Morgan's men, and will report to department headquarters at Dublin for orders.
V. Col. Basil W. Duke having reported for duty, is hereby assigned to the command of the brigade lately commanded by Col. D. H. Smith, and will at once enter upon the discharge of his duties.
By command of Brigadier-General Echols:
J. W. BRANHAM,
Acting Assistant Adjutant-General. (OR V39/2/816)

09 07 1864 [...day]

HDQRS. DEPT. OF WESTERN VIRGINIA AND E. TENNESSEE,
Dublin, September 7, 1864.
General S. COOPER,
Adjutant and Inspector General, Richmond, Va.:
GENERAL: I have now been in command of this department for a week, during which time I have been industriously at work endeavoring to inform myself of its condition. It is due to the Government and to all parties concerned that I should state that I have found almost everything in the worst possible condition. The troops are almost without organization and without discipline. When I reached here some 600 or more of the troops in the field were reported to me as entirely without arms, and, of course, valueless as soldiers. This state of things resulted from the fragmentary character of the different commands. The Kentucky troops being only the remnant, with the exception of a small brigade of the original control and of General Morgan, left after his raid of the summer of 1863 through Ohio, and his raid of last summer into Kentucky, and of the fragments of various regiments and battalions of Tennessee troops, which formerly constituted the brigades of Brigadier-Generals Vaughn and Reynolds. Some of these fragments were very small and were all thrown together; an attempt is still being made to preserve their original organizations. In the case of the Tennessee troops there is this also to be stated: In the month of May last these regiments, &c., all their under the command of Brigadier-General Vaughn, were ordered to Staunton by the late General William E. Jones, and all whose horses were in proper condition obeyed the order and went to Staunton from which point they continued in the command of General Breckinridge, in the army of Lieutenant-General Early, leaving however, in this department and in North Carolina some 600 men, whose horses were not in condition to be moved, and the various regiments and battalions have ever since been thus divided, producing the greatest confusion, probably more than half of every regiment and battalion and a part of almost every company, with a portion of the officers of each, being here, and the balance in the army of General Early. I am informed by General Vaughn that there are now in this department 900 of these men, and with General Early not more than some 400 or 500, the number of the first having been constantly increasing, and of the latter decreasing, many men coming through the lines of the enemy to the command here, and a good many, no doubt, leaving the command under General Early and joining the one here.
Of course not much can be done to organize properly these troops until the portions of the command in this department and in Early's army are united. I would respectfully suggest that the troops with General Early, known there as Vaughn's brigade, be ordered to this department, in order that the various regiments may be properly organized. I do not know that I have stated numbers with entire accuracy, as the records in the assistant adjutant-general's office of the department do not enable me to determine the strength of the various commands, no reports having been made since 1st of August, and then very imperfectly and unsatisfactory. I would also suggest the propriety of authority being given to me to consolidate some of the regiments and battalions, which are very small, which I think might be done with much advantage to the service and without detriment to the rights of individuals. I have not yet seen a roster of the officers of the department, there being none at the department headquarters. To show the lamentable want of discipline heretofore existing, I may state that some two or three weeks ago one of the regiments in the department refused to obey an order to move from their then location, and mutinied, and a captain and a large number of the men separated from the balance of the regiment, many of whom have not yet returned. When I assumed the command these facts were reported to me, and I at once directed the most active measures to be taken for the arrest of the captain and his close confinement until he could be tried and punished. This arrest has before this been effected, I hope. I have already taken steps which will insure hereafter regular returns from the command, and a full roster of all officers attached thereto; and I have also adopted measures which will insure a better state of discipline. Everything in my power shall be done to bring about a better state of things than «55 R R--VOL XLIII, PT II» has existed for some time as to the condition and effectiveness of the troops. In order to produce a thorough reform I need very much the services of one or two rigid and experienced inspectors, who, I hope, will be sent as soon as possible to me. I also need the services of an active and systematic ordnance officer, and I would be glad if one can be spared from Richmond, and that he would be sent to me, at least temporarily. I am endeavoring as rapidly as possible to make the reserve forces effective.
I have now three battalions of these troops, which have been organized in Southwestern Virginia, which could all be made quite efficient if they had not had the power to select their own field officers. They will at any rate, however, perform pretty good service I believe. The condition of East Tennessee is a very bad one, the large majority of the people being opposed in sentiment to us, and the country being filled with bushwhackers and marauders in organized bands. Murders are of almost daily occurrence on the persons of peaceable citizens, and enormities and atrocities are constantly being perpetrated. Some portions of Southwestern Virginia were also fast coming to the same condition, in a great measure, I think, in consequence of the inefficiency of the agents of the conscript department and enrolling officers in the region of the Southwest whose duty it is to see to the arrest and return of deserters. I am also convinced that the conscript laws are not faithfully and rigidly enforced in this portion of the State, there being many persons who ought to be in active service who have thus far escaped. I am now employing the reserves in driving out and arresting these deserters. Three days ago the enemy had about 2,200 men in East Tennessee, or this side of Knoxville, under command of Brigadier-General Gillera, a favorite officer of Andrew Johnson and Brown-ow. They have but a small force in Knoxville. In the Kanawha Valley their strength was, upon the last report to me, about 2,000, and a force of some 1,200 or 1,500 men near the Kentucky line. They are constantly making demonstrations from the one point or the other, but I hope to be able to protect the great interests of this region with the forces now here, unless the enemy should make a serious advance before I can bring about better organization and discipline than now exists, in which event I should have serious fears of the result. My principal apprehension is that now Atlanta is in their hands they will throw forward into East Tennessee a sufficient force to take permanent and entire occupation of that section, and advance into Southwestern Virginia as far as the salt-works. The corn crop in East Tennessee is a very fine one, and I am adopting measures to be ready to get the benefit of it for the Government in the event that we are able to take and hold possession of any considerable portion of that section. After the death of General Morgan I assigned Col. Basil W. Duke to the command of Morgan's old command, although he was not the senior officer in the command, and I am sure that he will improve its condition, as he is a most intelligent and efficient officer. I found Brigadier-General Vaughn in the department, and I have assigned him temporarily to the command of the troops in the field in East Tennessee, as I found that he had the confidence of the people there, and also the respect and confidence of the troops. I hope that the inspector and ordnance officer, whom I have asked for, may be sent me as quickly as possible.
I am, general, very respectfully, your obedient servant,
JNO. ECHOLS,
Brigadier-General, &c.

HEADQUARTERS ARMY OF (OR 43/1, 864-867)