It would make sense that the TurboTax program would alert you if the program thinks you are entering the form twice, however you don't say what the balance of the loans (both loan balances added together) is.
If the loan balance total is not over $750,000, the loans are secured by your main home, and you paid the interest, over-riding the program (because the two Form 1098's are so similar) that would be fine.
@jtrem714
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