Ginny --

If you have copies of all three dozen documents and cards in Garner's service file, they will show that his right leg was amputated by a Federal surgeon at Sharpsburg. The exact date of exchange isn't clear, but apparently he was returned by January of 1863.

The card you mentioned should read that James Garner's name appears on a Register of the Invalid Corps, P.A.C.S. [Provisional Army of the Confederate States], date of retirement, April 29, 1864; date of re-examination, Oct. 27, 1864.

Another document shows that he applied for an artificial limb at Richmond, Va., May 2, 1864.

Here are a few items about the 5th North Carolina at Sharpsburg MD. You can click on two different maps which show the regiment as part of Garland's Brigade on the battlefield. There are several different markers on the battlefield which mention the brigade and/or the regiment and its activities at Sharpsburg.
http://aotw.org/officers.php?unit_id=701

There's also a magazine article which provides further detail --
http://www.historynet.com/battle-of-antietam-federal-flank-attack-at-dunker-church.htm