Believe it or not, the e-filed partnership returns were accepted by the IRS when they were filed.  It took them 3 years to reject them, and let my client know that S Corp returns needed to be filed.

Now I'm fighting the IRS over penalties for late filing of S Corp returns for the client (as someone mentioned, this was the next thing to happen).  It has not been a fun process.  I've pointed out to the IRS that they accepted the timely originally filed partnership returns, and that the client amended to S Corp returns as soon as they were notified.  I've gotten them to waive the penalty for one year, but they're persisting in assessing penalties for the other.  It's so stupid - the wrong returns were filed, but they accepted them, and they were filed on time.  So to charge late penalties on the corrections is ridiculous - if they had rejected the e-filed returns when they were filed, this would have been straightened out years ago.

Definitely a big mess.