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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;
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).
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