After some more forum surfing, it appears another thread describes the problem in more detail and that TurboTax does not correctly calculate average or total balances when you have multiple 1098s after a refinance:
https://ttlc.intuit.com/community/investing/discussion/deductible-home-mortgage-interest-worksheet-2...
If this isn't fixed in the next few weeks I'll be using a different service to file, even if I have to re-enter all my information.
