if you save your profile settings (bookmark, pref.js, etc) in a directory other than your mozilla installation directory (eg: you save them in c:\document and settings\ instead of c:\program files\mozilla.org), your settings will be safe and sound.
if you save your profile settings in the same directory as your installation directory, then they will be deleted.
but yeah, to be safe, just do a backup of the files before you do un/re-install