I have this exact situation, in which I paid back money within the 60 days, but my bank (Wells Fargo) did NOT reflect this in the 5498. And I called them and they said something like "oh we don't report that information." so all I could figure out to do was to get the bank statements that show when I paid the money back, and now I have to amend my tax return and main the bank statements in to the IRS to show what was done. I'm not even sure where I'm supposed to put this "rollover" thing in Turbotax.
