I FINALLY had success with this.  The thing I did differently was merely try to e-file the amendment while in the return.  I usually only do it from the EF Center so I can ensure I'm highlighting the right line item with "amended" in the return type just to be sure.  When I tried to e-file while in the return, the amended version allowed me to check the checkbox to file that one.  To be sure it wouldn't change on me, I exited out of the return and THEN "amended" showed up in the return type, whereas it did not before.  It seems I had to trick the system into e-filing the amendment where the original was not filed by me.