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The easiest, safest way to sort this out is to get in direct communication with our Support Humans.
1 (800) 315-6664
1 (206) 523-4152
omnifocus@omnigroup.com

Which old thread are you looking at?

Here may be what happened...
If you stop using your iPhone for a while, the other clients have to cart around extra data until it catches up in the syncing again. Rather than do this indefinitely (and slow down syncing), after about 2 weeks the other clients drop that extra data and the databases become incompatible. At that point, you'll probably want to replace the iPhone database with the server database. But if you have any doubts, please contact Support.