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You can have multiple OF documents open at once, and the obvious case is the Archive. OF "knows" that the main database is the one that lives at Library/Application Support/OmniFocus/OmniFocus.ofocus and won't accidentally sync something else (and there's a check performed at sync time to make sure the two databases being synced have sufficient common history that would likely catch it if somehow it did).

Just double-click a different OmniFocus file to open it (or use the commands in the File menu for the Archive). You can drag projects and actions back and forth.