AY 2012-13 Actual TDS 1 lakh claimed 40000 only. demand for Msmatch of 40000 raised for 25000. refun

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Please visit your AO as per pan jurisdiction and state the above issues.....because CPC is only processing unit and can process those returns filed on website
In above case it looks like rectification return cannot be filed
So only way out is approach your AO as per pan jurisdiction who shall pass the necessary orders