Rectification XML for Intimation u/s 143(1)

Assessee was partner in a Firm(Audited u/s 44AB) and due date for ITR-3 was 31.10.19.

However ITR-3 filed on 13.09.19 without selecting the Nature of Business as Share of "Income from Firm".

Intimation received from CPC u/s 143(1) calculating late fine of 5000/- 234F.Intimation is stating due date as 31.08.19.

Now while uploading revised XML for rectification request the ITR Utility is adding late fine of 5000/- based on current date.
Please guide as to how to proceed in this case as late fine is not applicable.
Should I upload the revised XML with late fine of 5000/- or is there any other way out.