The EF center  error checking does not like when 2 files with the same EIN existin the EF Center I like to keep both the original file and amended file on my system. As you say, there's a duplicate EIN error.

I  change the EIN by one digit in the original return to fool Intuit.  Works but I have to make a note that I changed the EIN in the original (usually hit F8 or something like that

Or, you may be able to change the original (efiled) return so that it does not show electronic filing selections. That should keep it out of the EF Center but I'm not sure if it will work.