Ryan,
With the capture of the unmarked flag at Knoxville I would concur that they probably received a Fourth Bunting ANV flag upon the return to Virginia in the Spring of 1864. This was most likely the flag they used through the war's end and, as you noted with the flag lost at Knoxville having the colonel's name on it, they might indeed have found someone to paint on some battle honors.
Of course the brigade might also have been issued new flags with honors per the request of the brigade commander (I forget how long Humphries had the brigade from Chickamauga onwards). It will take a look at the other flags of the brigade to see if this was the case of the 17th was a loner in this respect.
Greg Biggs