This is a tough one guys and never seen anything like this. Here are the facts:

1. Doctor formed a PA with the State in 2019. An EIN was requested from the State for a Sole Proprietor.

2. Previous CPA filed an 1120-S  for 2019 instead of Schedule C. 

3. Tax payer paid themselves from what they thought was a corporation (because they thought they were) and all of the owner as well as employees were included in form 944.

4. State filing was done based on data in 1120-S.

After speaking with the IRS (I filed 2848), The 2019 return was rejected because the EIN was for sole Proprietor. thoughts on how to fix this mess!!