Yes, any amount you have to pay back can be included in your self-employed premium deduction. You can deduct all premiums paid, including the advanced tax credit payment, regardless of your circumstances for the year.
Please see Publication 502 and look for Premium Tax Credits. It gives an example that the amount of premium tax credit paid back can be deducted as a Schedule A medical expense. The same principle can be applied to your self-employed premium deduction as well.
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