I take it that you don't have any money (or much) left in the HSA, so you can't withdraw the 100% excess contributions that you made (see below).
In TurboTax, you'll need to tell the software that you were not in an HDHP for every month that you weren't.
This will generate an "excess contribution" screen. This screen will ask you if you can withdraw the excess by April 18, 2017. I am guessing you can't because of lack of funds.
So the excess will carry over to 2017. This has multiple effects;
- The excess is added back to taxable income so you will pay income tax on it.
- You will be assessed a 6% excise tax on the excess carried over to 2017.
- Your 2017 contribution limit will be reduced by the excess - but, of course, if you can't contribute any longer, that won't matter.
After you do this, yes, you can deduct the amounts you actually spent on qualified medical expenses on Schedule A (this may not be the exact same number as what you contributed).
