i installed firefox 3 on my laptop, bookmarks were fine & nothing lost. but on my desktop i lost all of them, but i was able import them back using this method, just locate the bookmarks.html file, inside your windows user profile folder.
C:Documents and SettingsKonataApplication DataMozillaFirefoxProfilesb8fvv704.default
plus i do bookmark backups once a month in case something goes wrong.