The muster roll for the bi-monthly periods:
Jul/Aug, 1863 records him as "Absent, missing at battle of Gettysburg, July 3, 1863"
Sep/Oct, 1863 records him as "Absent, taken at Gettysburg"
Nov/Dec, 1863 records him as "Absent with Leave"
Thereafter, bi-monthly reports exist through Jul/Aug, 1864, the last dated November 27, 1864. No mention is made of him, present or not present.
Prior muster reports January through June 1863, all record him as present.
It thus would appear that he never returned to his regiment.
The July, 1864 roster you note is not a Company muster-roll, but that of a Regimental Roster listing those who served in the regiment from it's organization in July, 1861. One roster lists him as a Captain, another as a 1st Lieutenant.
M323: Compiled Service Records of Confederate Soldiers Who Served in Organizations from the State of Texas