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The full error I am getting every time I start OmniFocus is:

Replace your database and start syncing?
Your current database will be backed up on your computer, and replaced by the sync database:

https://idisk.me.com/<username>/Documents/

I have turned Sync completely off and used a different location for the DB as I turned it on. Nothing I've tried has made any difference.

Best I can tell server sync is not working.