When dealing with a refi, you enter each 1098 individually one at a time, starting with the oldest loan first.
When you enter the 2nd 1098 for the refi, one of the screens will have a selection on it to indicate it is a refi. You must select that option.
Take note that since your mortgage balance on Jan 1 of the tax year exceeded $750K your interest deduction will be limited to the interest paid on the first $750K of the outstanding balance.
These points are only shown on HUD not on my 1098.
That's actually a good thing that your points are not duplicated on the 1098. You can and should claim the points as shown on the 1098.
When it comes to things like acquisition date, pay attention to details. The acquisition date of the home and acquisition date of the refi are not the same. Additionally, if you did the refi with the same lender, then your remaining points (remaining amortized costs) on the old loan are not fully deductible in the year of the refi. They either continue "as is" over the life of the original loan, or you can add them to the amortized costs of the new loan for deduction over the life of that new loan.
If you did your refi with a different lender, then your remaining amortized costs on the old loan are fully deductible in the year of the refi. Just work through the amortized entry for the old loan in the assets/depreciation section. If you do it right, then the program (not you) will show those remaining costs to be deducted in the Rental Expenses section as a miscellaneous expense.
