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If anyone's waiting for a solution here - I got a very quick reply from the support ninjas:

"The first step in resolving this would be to connect your iPhone to your Mac and backup your iPhone via iTunes.

Then, open this link in Mobile Safari on your iPhone: <http://people.omnigroup.com/kc/DebugOmniFocus/EmailDatabase.html>

This will allow you to email your OmniFocus for iPhone database, either to yourself or to us. Then, you'll want to sync OmniFocus for iPhone to the server copy. Meanwhile, if you emailed your iPhone database to yourself, you can actually open it on your Mac and compare your two databases.

If you'd prefer to have us fix this, and you don't mind sending us all the databases, we'd be happy to see what we can do to merge them for you. The sync database is a folder named "OmniFocus.ofocus" on your WebDAV server."

Robert