Did the corporation file 2553? 

I had a situation for 2020.  Client filed 2553 for 2020 in January but never got the determination letter.  Client had certified mailing for proof of timely file.

Came 3/2021, extension was rejected because "IRS record doesn't recognize it as S corp".

I paper filed the extension with certified mail.

In summer paper filed 1120S and e-filed CA Form 100S with 2553, showing "file pursuant to Rev Proc 2013-30" on 2553 (Lacerte Screen 38, Part 1),  In the explanation, the info that 2553 had been timely filed was included.

In September or October 2021 corporation got a late filing penalty notice.

In November 2021 corporation got the S status determination letter, effective Jan 2020.  

In January 2022, the penalty was waived.  

A happy ending...

I guess the processing of 2553 was just greatly delayed. 

By the way,  on Screen 3 "Explanation on top of form 1120, I also entered: "INCLUDES LATE ELECTIONS FILED PURSUANT TO REV. PROC. 2013-30".

Hope this helps.