Why did our refund drop by $2,000 after 1099-SA form entered and tax breaks section completed?

The 1099-SA records distributions from an HSA, Archer MSA, or Medicare Advantage MSA. If you took distributions from one of these tax-favored accounts, they must be for qualified medical expenses. If they are not used for qualified medical expenses and you are under 65, you get hit with a 10% penalty and you have to recognize the HSA distribution as income. If you're over 65 and they are not used for qualified medical, you don't get hit with the penalty. However, you do still have to recognize the distribution as part of your taxable income.

If your HSA distributions were for qualified medical, you may have accidentally indicated that they weren't during your interview for this form. May I recommend returning to your 1099-SA entries?