Rectification /revision of return after 143(1) assessment

HI,

My query is as follows-

A client had efiled an ITR for Ay 2009-10 . Due to an Data Entry error or an efiling programme error

Business Income as per BP sch is much higher as Itax and Donation has been added twice

But the Computation showed the correct Income hence return uploaded without any remark for Tax Liabitiy etc.

In Oct 2010 the intimation was recd with a Demand for 90,000/-which couldnt be understood why change in Income and raising of demand .

the reason for demand was realised  after 2 yrs whn Application for rectification was made to CPC  in Oct 2012 and confirmation also received to file rectification. But due to oversight it has been missed.

Now the It Dept following up for recovery ,but as such there is no liability,

The ITO not accepting Revised Return now What should the action be taken by the Assessee file a Revised Return or Rectification  and how physically or Efiling.

Please advice.

Thanks and Regards