I think I'm going to disassemble the upper and send it in when I ship the lower off to be engraved. I'm also going to go ahead and send in the Form 1 for the lower to get that in the works.
I spoke with a really nice lady named Robin at the NFA branch yesterday. I specifically asked her what would happen if I had a shipping issue and damaged or lost my lower while my Form 1 was processing. She told me that if I needed to change the serial number on the Form 1 prior to it being approved that I could just call and ask them to send it back to me for correction. When I send in the corrected form with the new serial number, it would go back in the box without me losing my place in line.