I filed Form 4868 on 7/15/2020 for a MFJ couple.  When I printed Form 9325 it indicates that a 1040 was accepted, Boxes 1 and 2. However, Box 6 is also checked stating that Form 4868 was also accepted.

When I update my clients' return with the final amounts, I get a message that the 1040 has already been accepted and that I have to submit an amended return, Form 1040X.  How do I proceed?