You don't say what you're financing. It "could" matter. Your primary home? @2nd home? Rental property that you own? Commercial property you own? You enter each 1098 one at a time.
When entering (and I can't stress this enough) *pay attention to detail*. I can't recall the wording exactly, but for the 2nd one you enter you'll select a checkbox on one of the screens to indicate that it's a refinance of the 1st 1098 entered. (or something like that). If you don't check that box, then the total outstanding on each 1098 are added together. If the total exceeds $750K that creates the issue you're already aware of.
Depending on just what was refinanced, it may also matter if you refinanced with a different lender or the same lender as the original loan. That determines how any amortized points on the old loan are treated.