I had someone ask me an interesting question the other day - he hadn't run BottomFeeder in awhile, and just wanted to purge all the cached items and have the next set of update cycles regenerate the feeds. It's a useful idea, and a feature I intend to add - but you can do it now, since I left a way open to execute Smalltalk code. Just pull down the System>>Execute Smalltalk Code menu item, and then write this:

RSS.RSSFeedManager getAllMyFeeds do: [:each | each removeAllItems].

Highlight that and hit ctrl-d - all your feeds will be empty, and the next update cycle will start refilling them.