I just noticed that RSSOwl seems to save its configuration (favorites & folders) at termination only. I had a short power outage (self-inflicted, but that's a different story) and when I restarted RSSOwl, all changes I had made since the previous start were gone. It might be a good idea to save RSSOwl's configuration more often, especially after new favorites are added and after changes to the folder structure.
This was already fixed for upcoming RSSOwl 1.2. Settings will be saved a short time after they have changed automatically.