There would have been 3 more bi-monthly musters for pay held before war's end. It is entirely possible that he returned to the regiment which was quite typical. Men quite often returned after quite lengthy absences. We just will never know.
It would seem highly probably he returned to duty, inasmuch as he brother continued in service.
R. O. Duffer, Private, Company C, 18th Regiment Tennessee Infantry, enlisted November 23, 1862 at Murfreesboro, Tenn., deserted January 16/23, 1864 [Jan. 28, 64' Co. muster roll]
Sept/Oct 63 Present, brother Brig. Tailor
Nov/Dec 63 muster roll missing
Jan 28, 64 deserted Jany 23, brother Brigade tailor
Jan/Feb 64 deserted from Dalton, Ga Jany 16, 64, brother Joseph absent, Brigade tailor with clothing department, Chief Cutter at Atlanta
Mar/Apr 64 muster roll missing
May 1 to Aug 31, 1864 brother Joseph, absent, in clothing department by order of Gen. Hardee ordered to report to Major Cunningham Jan. 4, 1864
No further muster rolls
M268: Compiled Service Records of Confederate Soldiers Who Served in Organizations from the State of Tennesse