On the screen immediately after entering (or editing) your 1095-A, you need to check the box that you were self employed. Then the program calculate the 'circle' and should put the proper amount on Line 29. So do NOT enter it again on Line 29, as the program does it automatically.
However, there are a couple of flaws when you are near the border of qualifying. In some cases, the program does not calculate things correctly. In other cases, the IRS rules don't give a clear way to do it, and the program doesn't do anything about it.
If checking the self employed box on the screen after entering the 1095-A does not qualify you for the Premium Tax Credit ('subsidy'), you may consider contributing to a Traditional IRA to lower your income, which would reduce the amount of the repayment. You can 'test out' various amounts of Traditional IRA contribution amounts until you reach a level that would qualify you for the Premium Tax Credit (the healthcare 'subsidy').
