I use Feed Wordpress on many sites and recently had a similar situation (some 700 feeds disappeared!). In my situation, a hard disk issue was causing a lot of server crashes, and the wp_links table in the database was not closed correctly and was hung. Running a repair on the table restored all my links.
FWP stores information about the feeds in the wordpress links, so you can check if this was te same situation by going to your links in the dashboard- in my case all of the links (one per feed) were gone as well.
It was a matter of going into phpMyAdmin and running a repair on the wp_links table (actually it is better to run a check on all tables, because our wp_options table was crashed as well).