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I have recovered from a time machine backup as I had a hard drive crash.

In between the restoration and the crash I shifted the omnifocus.ofocus file to my temporary hdd. Then, I used OF from there for a day and then went back to another hdd by restoring it and subsequently replacing the .ofocus file along with all sync files that changed, now I keep getting a popup that says

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


I also sync to the ipod but the OF is not running in the background.

When I did hit sync, it reverted to really old data.