I agree that you need to amend the initial tax return as that should have been filed on a 2015 tax return. I would include a letter of explanation as this will clearly be confusing to the IRS.
Regulation 1.441-1(a)(2) states that, except in instances related to a 52-53 week year (covered in 1.441-2), a taxable year may not cover a period of more than 12 calendar months. If you would file another 2016 return, you would clearly exceed this 12 calendar month rule. That unfortunately means amending the return.
While the IRS letter may have indicated the due date of the return, which is correct, I would be surprised if the letter indicated that actual tax year of the form to use in your situation.