If I had just read the Instructions for Box 6 at the bottom of the 1099-S, it says the same thing. So, I'll reduce the amount on the 1098, box 11, by the amount on the 1099-S, box 6, and report the reduced amount when I enter the information for the 1098 into TurboTax. I'll also check the box for "this amount doesn't match what's on the 1098" and give this explanation of the 1099-S from the settlement company reducing the deductible amount reported by the mortgage company on the 1098.
