I received an email from ITD about not deducting TDS on rent paid under HRA

A close relative recently received an email from the Income Tax Department about their ITRs for AY 2024-25 and earlier . They were paying around 60K/pm in rent to their landlord that they claimed as a deduction but were not aware that TDS has to be deducted on rent payments above 50k/pm.

What can be done to redress the issue now ? They can pay the applicable TDS with penalty and interest but how will the landlord claim the TDS deposited in their favour since his return cannot be updated now ? Won’t this amount to taxing the same income twice - once in the hand of tenant and once in the hand of the landlord ?

Any practical advice would be greatly appreciated.