sounds like you simply need to write to cubic s if you are confident that the backup is good, this will update the cubic s with the encoder data and other info from the backup
Use CS Config to confirm settings and data. You also may need to re zero then write again.
By the way I never recommend loafing a complete backup unless the controller was initialized. Even then make sure it's a backup from the same robot. Don't take one from a different controller unless absolutely necessary.