The other flag was described as "Portion of Staff and fringe." Sounds like some Union regiment ripped the flag off. (I believe that belonged to either the 31st Maine or 11th New Hampshire) both of those regiments did rip up one of their flags. Probably their National flags.
It is very rare, that any Union commanders admitted they lost a flag. Colonel Thomas, 2nd Brigade USCT admitted the loss of his brigade guidon, so I will take his word for it. A white lieutenant carried that guidon and was captured.
I believe many of the other "Unknown" captured flags, came from USCT regiment.
Have a good morning, Charles (good to hear from you)
Shawn