Thanks Indrajeet.

Under new portal one cannot choose schedules and complete return XML has to be uploaded.

While preparing XML for rectification AY 20-21 I am getting penalty under 234A = 25024 which is editable field.

In original it was only 1564. 

Should I correct it to what was in original as 1564 or leave it as it is 25024.

Please see attachment. 

Thanks in advance for any help.

I ALSO TRIED BUT IT IS SHOWING INTEREST AND PENALTY, BUT IF YOUR LAST FILLING IS ALREADY  REVISED IT WILL NOT CALCULATE INTEREST AND PENALTY, MORE THIS IS OFFLINE Return Data Correction, NO NEW INCOME OR DEDUCTION YOU HAVE TO CHANGE.  YOU HAVE TO SUBMIT UNDER THE SAME SECTION IN THE LAST ITR SUBMITTED AS PER 143 1 WHAT I FEEL THEY WILL JUST CORRECT DATA THE REASON YOU WRITTEN IN COMMENTS, MORE THIS CORRECTION IS UNDER 154 YOU WILL SEE ON TOP WHEN CHOOSE YEAR AND SUBMIT, NATURALLY THEY WILL ISSUE NEW ORDER WHICH WILL BE BASED ON OLD ORDER.  IF THEY ADJUSTED ANY REFUNDS YOU CAN ADD IN PAGE IT OF RETURN, CHECK YOUR 26AS SECTION C  Details of Tax Paid (other than TDS or TCS)  IF YOU DONT WANT TO TAKE A CHANCE WAIT TILL ONLINE RECTIFICATION START, WHERE YOU CAN CHANGE PART WISE

Read more at: https://www.caclubindia.com/forum/how-to-make-rectification-X M L-file-534249.asp

Selection of appropriate reasons while submission of rectification request is mandatory for the correct processing of the request by the Department. Please re-enter all the entries in the schedules. All the corrected entries as well as the remaining entries mentioned in the ITR filed earlier are to be entered. Make the necessary corrections in the data. While doing corrections, make sure not to declare any new source of Income or declare additional deductions.

Logically how rectification will carry late filling penalty, one can submit up to 4 year from intimation order. 

Read more at: https://www.caclubindia.com/forum/demand-notice-rectification-582431.asp?offset=1

I think wait for little more time, they will start on line rectification where you might be able to change IT and TDS page only.

JUST FILE EXACTLY THE SAME ITR  UNDER THE SAME SECTION OF YOUR LATEST ITR, MAKE CORRECTIONS OF MISTAKES, NO NEW INCOME OR DEDUCTIONS ALLOWED, DATA CORRECTION OFFLINE. YOUR UTILITY WILL CALCULATE THE PENALTY, NO PROBLEM  IGNORE IT, CREATE XML AND UPLOAD WITH REASON  OF CORRECTION, UNDER SECTION 154 NO PENALTY, I JUST RECEIVED NEW INTIMATION WITH REFUND, NO PENALTY IMPOSED. 

SEE YOUR SELF ATTACHMENT

@ Indrajeet Singh - if we upload the revised XML/JSON after ignoring this Rs. 5000 fine (levied by software) then do we end up paying this amount ? Or do the income tax officials recognise that this fine does not make sense ? 

Ignore for rectification under 154 no penalty , my rectification it was showing 1000 of late filling , but new order I got full refund. I already attached new order 

Aah thankyou so much !

The Rectification for FY 2019-20[ay20-21] is now working on the new Tax portal. Most important thing to note is to use Microsoft Edge for opening the new Income Tax portal. I was not able to do it using Chrome browser. After login go to Services>Rectification>+New Request>2020-21>Adv Tax/TDS/TCS entries as filled in the ITR will be visible.

Select the appropriate entry that need to be edited by selecting the Rectangle on left, then click Edit on top, scroll down and these entries will be visible for correction, after corrections click Submit and you are done.

ARN is generated and SMS is received immediately.