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When you compact the database, none of your actions or whatnot are deleted. All it's deleting is the history of how it got to the state it's in. OmniFocus should be compacting the database periodically on its own as it syncs with the server.

I forget all the gorey details, but if you're not syncing to anywhere, it might not do that auto-compacting. In that case, compacting once a week or so ought to do it.

If your database doesn't slim down, you might want to email our Support Ninjas (omnifocus@omnigroup.com) who could look and see if there's something nefarious going on.