I think that some of the Union flags ended up at West Point - I know many of the USCT colors did - and others that were left over were sent to depot warehouses for disposal or sale. The Jeffersonville, Indiana depot collected flags and I have a listing of those that still had in the late 1860s. Many flags were sold off as surplus - and considering that the Federal government was broke at war's end, they were selling off anything they could to get cash back into the Treasury including unit flags. You could get them for $5 or so.

West Point burned a lot of CW era flags in the early 1940s as they had no funding to conserve them. Most of the USCT flags were included. The ones that got burned were the flags in the worst shape. If you can find a WP catalog of their museum pre-1940 you will see what flags they had.

Three Tennessee Union flags were sent to the state in 1905 from the US War Department but are missing today.

Even though much of the CS War Department records were saved stuff still got burned up and that would include captured US flags. I have seen a number of allusions to that over the years. Things were so hectic at that time that stuff got left behind in the confusion.

Greg Biggs