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OK I just opened every backup in the directory from up to 5 days ago. None of them contain any of the information that was there, even the Omni Focus getting started project and actions are gone. Super frigging weird.

On a brighter note I just created an errand, backed up the file and quit, restored another (previous) backup and then restored this backup with the errand and it survived.

So I'm guessing the answer is to just rebuild it and hope it'll stay intact and backup like a mofo. Something happened in that upgrade process. That's all I know. Data lost but not contexts...I guess this should be added to the buglist for Snow Leopard. I emailed the support email as well about this.