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One way is to quit OmniFocus, go to the Library/Application Support/OmniFocus folder in your home directory and rename OmniFocus.ofocus (or possibly just OmniFocus if the extension is hidden) to something else. Restart OmniFocus, the default database will be created and the first sync will cause it to ask if you'd like to replace your database with the sync database. When you're sure that everything went the way you wanted, you can safely delete the renamed copy.