His regiment was declared exchanged "October 24th [1863], the Fourth and Forty-sixth [Mississippi] and General Pemberton and staff were announced exchanged."
http://www.gwest.org/46thmsin.htm

In as much as his unit re-assembled in Yazoo City, his home town, he had to be aware that he was obligated to rejoin his regiment. Apparently per muster rolls, he did not.

Not all muster rolls of Confederate units survived to be incorporated in the Compiled Service Records which were developed in the late 19th Century. Thus, we do not have an accurate account of individual pay records.

George Martin