If you were covered under the Payment of Wages Act, the answer would be simple: the maximum deduction from gross salary, including PF, ESI, etc., is 50%, so full deduction is not allowed. Furthermore, the deduction of excess paid allowances is considered a debt recovery, so it should fall under the other restrictions in the act.
However, I suspect you earn more than ₹18000 per month, so the act will not apply to you.
You need to read the standing orders applicable to the state where you work and understand the rules that apply in such a situation.
The question then arises: why was the allowance paid to you? It must have been listed in the salary slip, so you were aware of it. You can't claim ignorance. If the allowance was paid in error, it should be discussed, and recovery should be made in installments. However, if the allowance was paid due to a misstatement, manipulation, or fraud on your part, then the company is justified in recovering it in a single installment.
Your first step should be to speak with HR and your immediate manager to express your concerns about the unfairness of recovering the amount in a single installment. Now that it has been done, what resolution exactly are you expecting?