I got it all figured out. What was not clear to me was the the code which was being flashed was being flashed to the GPS xadow part, not to the RePhone part. Nothing was explicit about it, and I thought the gps part simply was the part on the xadow board. Once I realized there was a microprocessor on the GPS xadow board, I realized the flashing routine was referring to THAT part.
I have successfully flashed the updated code following the directions above, and the coordinates are correct for longitude now. I used a Adafruit 8266 Huzzah part.