Got intimation u/s 143(1) of the income tax act, 1961

You have received INTIMATION U/S 143(1) OF THE INCOME TAX ACT, 1961 for which. It is unlikely that you will get intimation for the AY for which you have two Form 16s.The last date for FY 2015-16 AY 2016-17 is extended.

Anyway suggest file revised return considering income from both companies.

It is for AY year 2016-17. As we all know that our PAN number is registered with IT department and they can check whether our return is correct. After getting Intimation, What i understood is, I have not submitted my form 16 of previous company and filed ITR with the help of form 16 of current company. so, I think they have checked and got to know the difference. I mean thats what i understood.

Dont file revise return while file rectification with reference No. mentioned on 143(1)

Now, here i have a situation. In the rectification request tab, they have mentioned under instructions, that, "A rectification should not be filed under change of income and a revised IT return should be filed instead". So what should i do now. As i have not uploaded my old form 16, which means, i have not showed my part of income from my side which income tax department already knew. 

In this situation, what should i do? should i go with the Rectification or should file revised IT return?