When you have rental property TurboTax requires you to enter the 1098 through the rental expenses section and then carries the remainder (if any) over to schedule A. When you also entered it into the deductions section the system assumed that you had another 1098 and doubled your deduction. So going back and deleting that was the right thing to do.
You shouldn't have to change the 1098. As long as all of your percentages are entered correctly into the system then it should take your deduction and put the rest of the interest on schedule A. It should communicate that fine.
Here are some good instructions for Air BnB owners using TurboTax.
@RichMM
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