Does the 8962 show 400%, or 401%?

As Rick says, your first step is to see if you can do ANYTHING to get income below 400%.  Between IRAs, SEPs and the other things Rick mentioned, is that possible?

Because the program is giving weird SEHI results, it seems very likely that it is possible without a huge amount of contributions (if the taxpayer can afford to contribute to a IRA or SEP).  That is most likely your best option, to avoid the full repayment.

If absolutely nothing can be done to reduce MAGI below 400% to avoid the full repayment (which seems unlikely), then just don't 'link' the 8962 to Schedule C on the 1095-A worksheet.  Then enter the actual full amount paid (including the repayment) on the spot on Schedule C for SEHI payments.