Income tax tax audit case financial year 2011-12

u will have to apply to the JCIT of your Jurisdiction / Range & take a special Permission from Him, then only you can do it, Else you will have to manage with your ITO to get issuing a notice u/s 148 so you will be able to file the return. 

Suggestion is Since its already 3 Yrs over now dont try doing all such things as it will be a sucdal act for you & your client, Rather keep quite & let it remain as it is status Co, & Prepare the Accounts in such fashion that they fall below TA limit & just keep going the way it is at present