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If you double-click on a .ofocus file in Finder, OmniFocus will open it up, alongside your "regular" OF file. So

1. Open OF as normal; this is your "local" version

2. Double-click the "other" copy of your OF file; OmniFocus will open it up in a separate window.

You can now select a folder, project or item and copy-and-paste between the two documents. If you choose View All Projects, and sort them in the same way, you can visually compare the two files.