Sounds like youre not marking for Amended EF correctly, it still thinks its an original.  And you really should be using the original file as the amended file....if you want to keep a copy of the wrong original, use Save As and give it a different name, but use that actual original file (with the original file name) and amend it.

https://proconnect.intuit.com/community/amend-tax-return/help/how-do-i-amend-an-individual-return-us...