Filing of Returns u/s 139 After Search u/s 132 Not Mandatory But is Beneficial !

Let us start with a practical situation. Say , in the month of June or July 2015 , search & seizure u/s 132 was  conducted on a group by the income tax department  . In that case , since the FY 2014-15 is over ,the tax return for assessment year 2015-16 was supposed to filed as per due date specified u/s 139(1) of the I.T.Act . But now that the search has been conducted , the assessment for the previous  year 2014-15 ( assessment year 2015-16) will be done under section 153A . So, a confusions  may engulf the mid of a tax practitioners  whether the normal tax return u/s 139 should be filed even when you know that the notice for filing of tax return  will be issued by the A.O assessing the income u/s 153A?