How we file updated ITR without penalty of Rs.1,000/- when assessee already submitted ITR but now submitting increased income with increased tax but below income of Rs. 5 Lakht

Hi,
I am seeking clarification regarding the computation of Section 89(1) relief for an individual who has received salary arrears amounting to ₹12,00,000 in FY 2024-25. The arrears pertain to the financial years 2019-20, 2020-21, and 2021-22, during which the individual did not file income tax returns. Salary received in the respective PY's are as follows 2019-20: ₹163,000 , 2020-21 - nil and 2021-22: ₹450000. Also he was having ₹1,50,000 deductions for all those years for which proofs are readily available.
1. Will it be wrong to consider those unclaimed deductions including standard deductions while arriving his tax on total income including arrears in the course of relief calculation?
2. He was having income less than taxable limits for the first 2 years ie. 19-20 and 20-21. But for year 21-22 his income exceeds 2,50,000. Whether non-filing of return attracts rejection of his relief claim?
3. Also in 10E filing , the form demands to fill the total income, should we show net income after deductions there?
4. Should i file belated return for Fy 21-22. Since ITR-U does not permit deductions and moreover, I have come across interpretations suggesting that deductions not claimed in an ITR may not be considered for relief computation , would it be advisable to avoid filing ITR-U for FY 2021-22 and directly proceed with Form 10E for relief under Section 89(1)?
Can someone help me out? Thanks in advance

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Regards

Dear Sirs,

We filed Form 1 under the Direct Tax Vivad Se Vishwas (DTVSV) Scheme on 31-01-2025. However, as of 06-03-2025 (beyond the 15-day timeline), we have not yet received Form 2 from the CIT. The portal status remains "Awaiting Form 2 from CIT."

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