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My EE isn't rooted either - see no need to do so.
Just backup what you see - books, apps that have the apk extension (they can be installed as opposed to installed apps that require special backup procedures to turn them into installable apps) and anything you think you want to keep.
I seldom use USB to copy anything to/from my EE because using ES-FileExplorer either in LAN or FTP mode is easier - don't need to be near a computer.
If you follow the instructions and double check everything there is nothing to really be afraid of.
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