You should have the user recreate the bookmarks. The old db is corrupt, so its items are of no value, although making a copy is probably a good idea in case this turns out not to solve the problem.
You’ll have to close down the user’s Notes client completely, then delete the db from the “Data” directory via Windows Explorer. When the user signs back on, Notes will create a new bookmarks db, and the user can open each database and create a bookmark for it. It’s a major inconvenience. About all you can do to simplify it is take a screen shot of the bookmarks list before deletion so you know what to replace.