Accidentely e-filed an amended return using regular e-file option. Will this be a problem?

When was the original return filed? And was it paper filed?

If the original was efiled you should have gotten a rejection when you “efiled” it again.

The taxpayer e-filed it through a self-serve online software.  When I filed it originally, everything came back as accepted.

I tried calling Intuit today and what they told me was that they can’t see what was sent, but they believe that if I used the normal e-file option that the 1040-x would not be transmitted even though it is listed in the filed section of the e-file screen.

They had me unlock the return and submit it through the e-file amended return option.  I am worried now that submitting it through both options is going to become a problem.  

They were not very helpful.

Something doesn’t add up. If the client efiled their 1040, and then you efiled a 1040, your submission would be rejected becayuse there is already a 1040 in the system for the taxpayer. Are you sure client efiled their return? Are you using the same SSN they did?

Yes, I have a copy of the original return that they e-Filed.  I cannot say why it would accept it, but the client confirmed that both returns were e-filed originally.  I have confirmed that the original return’s SSN match the ones that we sent.