Defective return

 Assessee ( Salary assessee) filed return on 13-11-2015 for AY 2015-16.Return showed Rs. 1300 payable and not remitted while filing return.Return treated defective and communication dt 16-11-2015  via e-mail sent to assessee from CPC, Bangalore to remit tax and rectfy return.This notice  remained unnoticed by assessee and the same  notice was received by post two weeks back .Assessee now detects that actually some deductions  like HRA exemptions were ommitted to be included in the original return and the return  resulted in a demand instead of refund  of about Rs.16000/(Refund would have resulted had the dedctions been included in original return.) Defect as pointed out is not rectifed till date.Since the original return was filed belatedly, what is the way  to include the deductions ommitted and claim refund? Can assessee file a fresh return ( not revised return)?. No communication has been received from assessing officer concerned.