Why filing of amended return from the back-up file?

The back-up file should only be for you to have a record of what has already happened and you do the amending to the original file and efile the now corrected original file.   (My back-up file is the paper one in my metal file cabinet.)    

By sending the amended from the original it has the other info imbedded in the transmission that should make it accepted.

Good luck in several weeks when IRS decides to reopen.