Did you by chance change the taxpayer?
I did this when I had a client get married and they wanted to be the spouse not the taxpayer. It caused that error and we couldn't find it because the social is not duplicated.
I don't remember exactly how we got it fixed but there is a home base updated or a file repair or something along those lines that needs to be run. ProSeries still had the spouses ss as taxpayer so it recognized duplication when trying to efile and gave me that error. Once ProSeries pointed me to the right place and ran the update it changed the hidden social to the new taxpayer social and it efiled just fine.
Just a thought that this might work in your case.