You should be using the same file for the amended as you did for the original, you shouldnt have 2 files in the EFCenter with the same SSN.  If you amended using a copy, it wont be able to Efile, it needs to be the original file with the embedded original EF data.

If you saved a copy of the "wrong" original with some other name, open it back up and uncheck the Efile boxes on it, so it kicks it out of the EFcenter.