Updated Return becomes Invalid

This query is : Resolved 

08 July 2025 Individual having salary income 1,80,000 and ₹5000 Interest filed ITR U for A. Y. 23-24. Late Fees of Rs. 1000 has been shown as Additional Tax Paid. No Original Return was Filed. So, the Whatever Income Offered in ITR U (Updated Return) is Additional Income. While Filing No Validation Error shown by Income Tax Portal and ITR is E-Verified immediately. Later, Dept. Made such ITR Invalid stating that - "As seen from Sch. Part B-ATI of the updated return filed by you, the same results in a refund. Hence, in accordance with clause (c) of the first proviso to sub-section (8A) of section 139, the said updated return filed by you is invalid, ab-initio, and is deemed to have never been filed."

But, I have not claimed any Refund in ITR.
Is Income is below 2,50,000 - that's why it is considered Late Fees ₹1000 Refund?
But, without ₹1000 Late Fees IT Portal Showing Validation Error after we Paid Late Fees and put Challan Details in ITR U then It accepts.
What Can Be The reason of such Invalid ITR Treatment?

08 July 2025 As income was below basic exemption limit, there was no additional income. Updated return cannot be filed if there is no additional income.


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