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It depends on what caused the failure though. If the kobo stops working due an error in one of the books, misconfiguration in the config files, or corruption in the database,, restoring the files from your backup will work.
However, the Kobo operating system itself is not accessible to Windows when you attach to usb, so corruption of the system files (either due to hardware failure or botched update, or somehow attempt to replace / patch the system) will not restore form your file backup
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