Normally, if actual papers for Courts-Martial survived then they would have been included with the Compiled Military Service Record (CMSR). What is in your ancestor's CMSR a card where your ancestor's name was mentioned in an original list or record that had other soldier's names listed in it. These ledger books of the Adjutant & Inspector General's Office are in the National Archives and contain the information that I will list below.

Lane, Charles H. Private. Company D, 43rd Georgia Infantry. Trial 21 DEC 1863. AWOL. Punishment: Hard Labor.
SOURCE: Roster of the Courts-Martial in the Confederate States Armies, by Jack A. Bunch. White Mane Books, Shippenburg, PA, 2001.

The General Order number you saw in the CMSR is when the list of the most recent Courts-Martials were confirmed and sentences were being carried out and then list sent forward to the A&IGO.

I hope this helps.

Respectfully,

Gerald D. Hodge, Jr.
War Between the States Historian
Historian: 39th Georgia Volunteer Infantry Regiment