[whpalmer4]

No, whenever a sync happens all of the changes should be transferred. If you started the iPhone sync before the desktop sync had finished, you might not get the new changes until the next sync, but your multiple syncs should have taken care of that.

Before it changes any more, why don't you zip up a copy of your OmniFocus.ofocus file from MobileMe to preserve the transaction history. Then send email to the support ninjas or give them a phone call. There are some cases where the iPhone will sync but not appear to get the updated data, but they are pretty localized and it seems unlikely that they are the explanation for what you saw.

I've noticed that if I have an action from my Inbox displayed when my iPod syncs, and the sync brings over a change to that action, the display will not reflect that change, even if I go view some other Inbox action and return. However, if I go to the home screen and then return to the Inbox, the data will be up to date. If I'm looking at an action in a project, I have to go back out to the Projects screen and back into the project. Something to be aware of, but not likely to be the explanation for what you saw.