Ben,

The bulk of these flags would have been sent to the US War Department. If you need a book listing of the captured CS flags in that repository seek out online a copy of this book:

The Returned Battle Flags - Rank & File Publications - edited by Richard Rollins

Such flags as made it there are listed in this book.

The other option is to go to the National Archives as they have the hand written original listing of the over 500 CS flags.

Greg Biggs