I think it matters if the repayment is owed or they sold at a loss.
If payment is owed, I would certainly try to get credit for the $3000 already paid. But if the payment owed is less than $3000, they won't get a refund, and then using the $3000 here would stop them from claiming a refund by amending 2014 and 2015.
If they sold at a loss (which seems more likely since they sold after just one year, once you add in the closing costs and subtract the commission) then claiming the payments won't get them a refund since it's over the 3 year limit.
