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If you're running current versions of the app, they should all just manage the clients automatically.

If you do go rummaging around in your files on Omni Sync Server, please be cautious. Another option is to contact our ninjas (omnifocus@omnigroup.com) if you're having slow syncs or some other problem. They can look at the structure of your database (without seeing individual actions) and tell if there's an old client clogging things up.