I do the same as Terry.  I have no use for a computer file of the original return that's wrong.

But to answer your question, that Save As file, name it  JonesTomOriginal.20i (or something similar) and then uncheck the EF boxes on the fed info worksheet, bounce over to the state return as well before saving and exiting, that removes it from the EFCenter. 

Now open up the file with the original file name (JonesTom.20i) and activate the 1040x (and state amended) and then make the changes.

That way when you transfer the files over next year, you'll still be using the JonesTom.21i file for the clients return.