I filed my clients federal extension in July, 2020 for 2019 and it was accepted.

Now I am trying to file the 2019 federal return but it will not accept because

the IRS is saying that it already has a return with the same tax payer ID.

Was there a box that was supposed to be checked for the regular submission

to let the IRS know that this is the actual filing now?

Please advise. Thanks