E-file a superceded/amended return?

To resolve this issue, you'll need to file the return from the same file that contains the original return.  

I typically make a copy of the return and append the name with "as filed" and then create the 1040X in the original file. 

In addition, I usually make a comment on the return status page under other that states "Amended".  This, of course, doesn't affect the return but it just provides an additional safeguard for me and any staff that might work on the return in the future.

Creating the amend in the original file will allow the successful e-file of the amendment/superseded return and also ensures that when you transfer the file over to ProSeries next year, you have the amended file as your base for things like carryovers, etc. that may have changed during the amend process while preserving your initial file name.  

Since you made a copy (I never make a copy, I always use the original file) you need to go back to the original file and uncheck the EF boxes, remember to switch over to the state after you uncheck the boxes, before you save and exit.