Neither the 20th Georgia nor 158th New York have unit histories that I have ever found.
Not all unit histories mention captured flags either based on my years of experience!
Sometimes you need to go to letter collections, diaries and period newspaper accounts to find captured flags for both sides. And this is why it takes so long to find stuff!
So far as 40-50 Union flags being lost at Chickamauga - that's too high from all that I have read.
have you consulted with park historian Jim Ogden? if you, you certainly need to do so on this.