Rectification u/s 154

Hi friends

Need ur guidance on following matter.

In one of our client case we have e filled the return for the A.Y 10-11.

Income tax department issued intimation u/s 143(1) without considering the depreciation

We had filed online rectification on above matter but the rectification is rejected by CPC now they have released the refund amount after deducting tax impact on depreciation.

now i cant file the rectification again so what is the way out now?