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Get your taxes done using TurboTax
I am not sure I understand your point.
If you owed some Premium Tax Credit back, this will appear on line 2 on Schedule 2 (1040). Did this not happen?
Since you were self-employed, when you entered the 1095-A, you should have been asked if this form is associated with a business (I hope you entered the business first, so TurboTax can ask).
Note that self-employed taxpayers can earn the Self-employed Health Insurance deduction (line 16 on Schedule 1 (1040)) for premiums that you paid with after-tax dollars (one of the columns on the 1095-A, and any Premium Tax Credit that you had to pay back.
So I haven't checked, but if you have an amount to repay on your PTC on line 2 on Schedule 2, it seems reasonable that the amount on line 16 on Schedule 1 be increased by the same amount. Did this happen?
Let me know if it didn't and I'll test it.
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