jameswilson
The server manager backup to desktop is usually of limited use as it may not successfully backup a system with a lot of data on it, so do not use that (typically).
The correct backup to perform is:
Login as admin to the admin console, then select Backup to USB drive
That will create a full backup as a smeserver.tgz file.
You can then use that backup (on USB drive) to Restore from at first boot after installing a fresh sme9 operating system.
Early on during the first boot, you will be asked if you want to Restore from backup, then insert the USB drive only when asked.
Do not connect any USB drive when installing the OS, as it may be formatted etc.
See
http://wiki.contribs.org/SME_Server:Documentation:Administration_Manual:Chapter6#Option_8:_Perform_backup_to_USB_device