Regarding relief u/s 89

Sir, my friend received salary in arrear. He filed form 10E and claimed relief of Rs. 33629/-. After that he filed his ITR and claimed relief u/s 89 same amount in ITR. After processing the return he received intimation u/s 143(1) in which cpc has taken relief u/s 89 Zero and has refunded only Rs. 12000/-. what should he do? Please suggest and explain the same.