Rectification in return

Hello,

My colleage has filled Return for AY 2015-16 [FY 2014-15] filled return after Due Date, In that FY he has changed 2 Jobs, and in both jobs TDS has been deducted and also shown in AS26. In his ITR he included 1 job salary and considered TDS of both the jobs. Now he has received question from the department about the mismatch of income.

Since ITR is filled after due date so we cannot file Revise ITR. So what can be done next?