The best way to enter multiple 1098s due to a refinance is to add them together - to create one 1098 out of them. The amount of the property that is financed should just be one number since the two forms are for the same property.
I would advise you to amend the tax return and go back through and delete the 1098s that you originally entered and replace them with the one combined 1098. This should give you a correct value and show the amount that you should have paid. Filing that return and paying the taxes due will solve the problem (although you may still receive a bill for penalties and/or interest from the IRS).
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