[Brian]

iTunes backs up your phone from time to time, and this includes your OmniFocus database. I'm not actually sure what, if anything, can be done at this point; you'll want to mail the support ninjas and we'll see what we can do.

The expected way to take care of this would be to use the iTunes restore feature and then just launch OmniFocus. If you restore again from your most recent backup, does OmniFocus behave as expected?