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The sync mechanism has a "last change wins" conflict resolution system, so if changes are made on both desktop and mobile client, after the sync the state will reflect the system which changed that action/project most recently (unfortunately, in your case, that's the system that deleted the project). Otherwise, if you changed the same item differently, OmniFocus would have to have some way to ask you which version of the change you wanted. Changes are done on a per-record basis for efficiency (due to the relatively wimpy processor in the iPhone) so changing the title of an action on one device and changing its due date on another is going to result in one of the changes (whichever was made first) being lost when both devices are brought into sync.

There's a lot to be said for syncing any device you use as soon as you've made some substantial changes! Had you done so, it might be possible to recover your changes even if they didn't get captured by a backup of the OmniFocus database, so long as the database didn't get compacted.