That was the question running through my head, too. Have you recently backed up your library? If so, then the risk seem (to me) to be minimal, though I'd check with Tech Support or one of the more savvy Forum-ers first.

Also, where are you in the process? Has the EE rebooted already?

I read through the EE documentation and the previous posts on library migration, and I don't see anything too relevant. Boris did mention that only the library gets migrated, so I guess you shouldn't have to worry about losing anything but your data (as though that isn't a huge problem :/ ) Good luck, and let us know what happens.