Because your favorites folder in the Effects tab will always be emptied when trashing prefs (or upgrading) (yes it is un the manual), You could create an Effect’s Project that will contain just those.
Drag your favorites Folder into the browser of that project and save it.
And back it up somewhere else.
And DO get Pref Manager as said before.
Hope this helps,
Patrice Freymond
Senior editor
FCP Certified Trainer
patrice@monteur.tv