Most of the missing numbers were sent to the Southern states themselves if the War Department could ID the flag before its return.
Several were "loaned" by the War Department to various Union unit reunions - most were not sent back. The 28th Virginia flag taken at Pickett's Charge remains in Minnesota today after its "loan" to an early 20th Century reunion of the 1st Minnesota Infantry. I consider this flag to be stolen Federal property. Some of these flags have ended up in private collections today.
Greg Biggs