How does TT handle HSA contribution made for previous year that is also listed on 5498-SA for current year?

I made a personal HSA contribution in 2017 which was correctly applied to 2016, and reflected correctly on my 2016 5498-SA in box 3.  The amount is also listed on my 2017 5498-SA in box 1, but if I enter it as a 2017 contribution that would end up being wrong, I only made the one contribution, especially since I wasn't in a qualifying HDHP in 2017 and was not qualified to contribute anything for 2017.  Do I just subtract the amount contributed for 2016 from the amount reported for 2017 before entering in TT, or will the question be asked somewhere down the road and the situation corrected?