Resolving Compliance Issue for notice received after due date

Sumit Chauhan   10 April 2021

I had received a compliance related email on 2nd April for AY-2020-21. This was regarding missed savings interest declaration. However, notice shows generated date as 28th March.

I acknowledged the issue on the compliance portal and paid the tax after filling the details on the Income tax portal , however, I'm not able to submit the revised declaration now as the due date has passed (31st March'2021). 

Considering that I received the mail itself after the due date, how can I now submit revised ITR. Does it need to go in belated category now with penalty?