Combine the two 1098s into one. The IRS has received a copy of both 1098s and they understand that the points are deductible to you so it's not a mystery. The software just isn't recognizing that it's all the same loan. So create one 1098 with the combined mortgage interest and points. Don't combine the loan balances, just enter the balance from the most recent 1098. Then everything should line up.
@flyfresno
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