Sounds like you did it right.

As long as you used the file that was originally accepted, there shouldn't be an issue...its when you use the copy that things get weird because the EF data doesn't get saved in a copy with a different name.

Maybe you goofed and used the wrong file?   You may be stuck paper filing that second amendment.

I stopped making copies of the wrong file, I save a PDF or print out, but if its wrong I no longer need a computer copy of it floating around to get mixed up, I keep 1 master file per client with the same file name structure for everyone that rolls from year to year.