I have been reading with interest this thread regarding the desertion/reinlistment of your ancestor. My ancestor, Pvt. Benjamin Griffith Charles, Co. A, 65th Georgia Infantry, was in a similar situation. He received a sick furlough and left his unit on Feb. 23, 1864. He was never able to return to his unit and was listed as a deserter. However, he was able to prove that he was not a deserter in that he tried to return to his unit in May, 1864, but Sherman was already on his way to Atlanta and was between Ellijay and Gen. Johnston's Army. Pvt. Charles attached himself to the first Confederate unit he came upon, the 4th Georgia Cavalry, which was operating to the east of Gen. Sherman's Army. Before the 4th returned to the main Confederate army, (hers is the part that may shed some light on your ancestor) the order was given for ALL Confederate soldiers detached from their commands who were then north of the Chattahoochee River to form with Gen. Wofford and the Georgia State Troops. This was done to enable many of those who had been seperated from their units, for a variety of reasons, but many for desertion for going home to their families in North Georgia, to return to service with no questions asked, and to get trained men into these units which were being formed from old men and young boys to help defend Georgia. My ancestor also surrendered with Wofford at Kingston. Being listed as a deserter, he had to prove he was not to receive his pension. In the pension were letters from men who fought with him in the 65th Inf., 4th Cav., and with the state troops, as well as a letter from the man who came with his father to Dalton from Ellijay to take him home. I believe your ancestor got his pension based upon the entirity of his service, but the witness letters were only from the latter unit to prove he was not a deserter from the 65th. His records of service with the 65th would have been on file and he would not have needed proof of that service in the form of witness letters from comrads.
Checkout the web page for some great research on the 65th Georgia Infanty (This is NOT my website!)