I got through to Intuit support. They did a screen sharing session with me. We watched as my refund shrunk by almost $10k when I added in the second 1098 from my refi loan. I pointed out in the worksheets that the principals are added rather than averaged. They called me back the next morning and admitted the bug, as well as the magnitude of it. They said the website would be updated in around 3 weeks (so mid Feb sometime). We'll see.
In the meantime, you can replace your multiple 1098s with a single, manually-entered one that sums the interest paid across the individual 1098s. Check the box that says "The interest amount I entered is different than what's on our 1098." You can then provide an explanation like "TurboTax has a known bug where multiple 1098s aren't calculated correctly. Workaround is to sum the interest paid into a single 1098." I'm told (but can't verify) that the IRS won't come after you as long as the values are right, even if the 1098s don't exactly match. Do so at your own risk. Hopefully this workaround will be moot in a few weeks anyway.
