I did the same thing you did and was still shorted on my interest deduction after entering zeroes on the balance on 12/31/2020. Same scenario of owning two properties with one being refinanced and having two 1098s for one property. I think part of the problem is my refinance loan went into effect 5 days before my old loan was paid off. Regardless, I never actually owed for more than one property between the two 1098s. TT does just calculate the totals of all the mortgage balances which pushed me well over the $1 million mark short changing my total interest deduction. I concur TT needs to fix this.
