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I don't know for sure, but my impression is that there are supposed to be multiple client files now. I see a new one get created every time OmniFocus on my Mac syncs. And they get cleaned up after a period of time (an hour or two later).

Yes, the really long sync times are a problem (one which I haven't seen personally). But I wouldn't read too much into what files or how many files are floating around inside your database package. That's Omni's turf and only they know the true inner workings of the app. In other words, I'm not so sure the "Lizard Hack" is still valid with the most recent sneakypeak builds.