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saswatabanerjeeIf the company deducted and paid higher tax due to mistakes of its own internal procedure, it is the fault of the company and not yours. The law requires them to compute and deduct tax evenly through the year. In case you do not submit the tax proofs then in the last few months they can deduct higher. It is really stupid for someone to say they do not consider proofs given in December and will only consider it in February
It appears to me someone messed up and are trying to recover the money from you.
One thing you need to check is whether the money has actually been credited to your 26AS statement on the income tax website. that would mean the money is paid to the tax authorities and you can claim it back when you file your returns. Please remember that you need to file your returns in any case, even if you plan to study abroad.
How you deal with this is now up to you. You will need to show this experience later and it may create a problem in the BGV at that time. However, paying them ₹ 2 Lakhs is a heavy amount, specially when it will be at least a year before you get the refund from the income tax authorities.
From India, Mumbai