You will need to mail a paper copy of the 2016 income tax return to the IRS. I recommend that you use certified mail, return receipt requested.
If you have proof of filing (such as a certified mail receipt or proof of electronic filing), you should send a short letter explaining that you timely filed and paid and have enclosed proof (copies, not originals) of timely filing and payment.
If you do not have proof of filing, then you could possibly be assessed a penalty for late filing. However, you may request an abatement of the penalty, if assessed.
Please see the following link for instructions on where to file your return: https://www.irs.gov/filing/where-to-file-paper-tax-returns-with-or-without-a-payment
If you still aren’t sure what happened with your 2016 tax return, contact an IRS representative at IRS Tax Help Line for Individuals - 1-800-829-1040 (TTY/TDD 1-800-829-4059).