I have been through the OR in detail for CS flags taken at Missionary Ridge but not US flags. In fact, Lee White and Jim Ogden and I sat down for a day a few years ago and we have the most complete listing of CS flags taken at Chattanooga/Missionary Ridge there is. all based on reports and some other details.
We never did go into the captured US flags, although this does need to be done.
Gerald's book suggestions work and you might try the Spruill's tour guide as well.