In TurboTax, there is no question asking "Were the points reported on the second Form 1098 also reported on the first Form 1098?"
It seems silly to me that the points would be reported on both Forms, since the interest paid is allocated.
Regardless, when using TurboTax, please enter the points on the first Form 1098.
If the first 1098 is for the original purchase, you will need to select how you wish to claim, all in one year, or throughout the life of the loan.
Pub 936
@th3ngineer
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