You need to enter your calculated interest in a different way. Any forms with errors will prevent you from e-filing your return (and invalidate the TurboTax guarantees). This includes numbers in a red font, red boxes, or exclamation points beside the form name in Forms Mode.
Use the step-by-step process if you can. When you click Done at the bottom of the 1098 Summary page, you should at some point be presented with a page that says your interest deduction is limited. This page also presents a box where you can enter the interest deduction you have calculated. This is the best way to override the interest calculated by TurboTax.
Your other option is to delete all 1098s except for the most recent, active loan (with a mortgage balance under $750,000). Enter your calculated interest on this 1098. While this is not the best option, the other information you enter on this 1098 is not reported to the IRS. As long as you can prove your calculations, consolidating your entries in this way is acceptable.
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