The 61st Virginia was not in BG. Wise's Virginia brigade. The 61st Virginia Infantry Regiment was raised at first Eight companies under the "7th Battalion Virginia Infantry". They just needed two more companies to become a full regiment, they did and they were eventually put in BG. Mahone's all Virginia brigade.

By the time of the Petersburg Campaign, Mahone had been promoted to Major-General and commanded the third division of the 3rd Corps under LT. General A.P. Hill. MG. Mahone's division contained the following brigades at Appomattox (3-9 April, 1865).

BG. Forney's Brigade, 8-9-10-11-13 and 14th Alabama infantry regiments.
BG. Weisiger's Brigade, 6-12-16-41 and 61st Virginia infantry regiments. (Mahone's old brigade)
BG. Harris's brigade, 12-16-19 and 48th Mississippi infantry regiments.
BG. Sorrel/Colonel Tayloe's brigade, 3-22-48-64-2nd Battalion-10th Battalion (All Georgia infantry regiments).
BG. Finegan/BG Brevard/Col Lang's brigade, 2-5-8-9-10-11, Bonaud's (GA) Battalion (mostly all Florida regiments)

Upon looking at maps on the final battle at Appomattox, I don't believe the 61st VA lost their flag in a battle, but surrendered the flag when General Lee surrendered his army.

Here is a link to the Civil War.org (Maps) Notice to the right, Mahone's brigade.

http://www.civilwar.org/battlefields/appomattox-courthouse/maps/appomattoxmap.html

Well I hope I helped out a little bit.

Have a great day,

Shawn Prouty