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I setup a Bonjour sync, everything worked fine. I changed some times on the iPhone4, synced to desktop, all is good. Made changes on the desktop, synced back fine.

I checked off three items on the phone and now get a message on the next sync with the two options:

Keep Device Database
Keep Sync Database

Which do I choose?
harringg, you'll want to give our support ninjas a call (800.315.6664) or email us; that dialog shouldn't show up unless sync has been turned off and back on on one of your devices or something.

Somehow, it sounds like the device in question has fallen out of sync with the server. Once that happens, OmniFocus can override the database on the server with the one from the phone (or vice versa) but it can't merge changes between the two.

Not sure how that happened, but if you contact the ninjas we can determine what happened and help you prevent it from happening again. In the meantime, I'd just hit "Cancel".
Support email sent. I was really excited to see OF on the iPhone and the first few syncs went off without any issues.

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