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If you want to just delete all your site preferences you can do so by opening the bookmarks page and then click on the "Site Preferences" collection in the sidebar to the left. Deleting the entries in here will remove the site preferences for the site.

Also, locations of all your OmniWeb support files:

~/Library/Application Support/OmniWeb 5/
(The main support files folder. Stuff like your bookmarks, bookmarks collections, history, workspaces etc.)

(OW's preferences file.)

(The cache folder, the main Cache bundle for OmniWeb 5.1 and stuff like favicons.)

(The OmniWeb 5.5 disk cache)

We'll look at consolidating the last two but for the moment they're separate.