Hi Shawn,
It is very possible this could be the flag of the 51st North Carolina regiment. They lost their flag that day during the fighting in and around Fort Harrison. They were reissued a fifth bunting issue ANV flag soon afterwards which survived the war and is part of the North Carolina Museum collection. Here is what Michael "Howie" Madaus wrote concerning this flag:

"One other document has recently been brought to my attention. In the 1949 issues of North Carolina Historical Review is an article by Thomas E. Blades and John W. Wike entitled "Career of a Flag". This is the story of the U.S. flag carried by a company of the 12th U.S. Infantry from North Carolina in the Mexican War. The staff of that flag was later used by the 51 st North Carolina. To quote page 444 of the Review-.

"Prior to the burial of the standard [U.S. flag of the 12th U.S. lnf.], Cantwell's brother, John 1. Cantwell, a colonel of the Fifty-first North Carolina Troops, Confederate States Army, had taken the staff off the flag and placed the colors of his regiment upon it and these had been captured by Union forces in Virginia."

I have not been able to locate that staff, which (I presume) would identify the flag that the 51 st North Carolina lost at Fort Harrison on 30 September 1864."