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The sqlite lite database can be found at:

The core database (~/Library/Application Support/OmniFocus/OmniFocus.ofocus) is stored as XML in all those zip files you mentioned. But an sqlite database cache is generated on a regular basis (every launch?). Presumably, it's used to help with searching and sorting performance.

Also keep in mind that accessing that sqlite db directly is probably unsupported and undocumented. Proceed at your own risk.