Thats because you made a copy. 

IF youre going to keep a copy of the wrong original:

Lets pretend your original file it names JonesTom.20i

Open JonesTom.20i and Save As JonesTomOriginal.20i and uncheck the EF boxes on it, that takes the copy of the original out of the EFCenter.  Be sure you open the state return (if applicable) before you save and exit that copy of the file.

Now go back to the EFCenter and open JonesTom.20i and activate the 1040X by putting the year in at the top, then you make your changes.