@dbergman suggest just calculating the interest yourself (seems you have a good handle on that) and enter that figure in the 1098. The IRS is not going to care that you report a lesser number as you are taking a deduction less that is reported on the 1098 and you'll have your manual calcuation to support how you came to that conclusion.
you can use the worksheet on page 12 of the attached to get to the exact result. Start with Line 2- you have no 'grandfathered mortgages'.
https://www.irs.gov/pub/irs-pdf/p936.pdf
Assuming a fixed rate loan, you can take the interest and divide by the interest rate to get the 'average mortgage balance'. it should be similar to a two point average but may give you a better deduction - slightly. (left side of Page 13)
Alternative: call support and have them walk you through this (they can screen share)
