Next time ensure you've taken a copy of the files you see when the Kobo id attached via USB. NickelMenu stores all it's configuration data in the .adds/nm directory of the drive; I'm not sure about KoReader. If you're using a Mac you will need to select a Mac option to display hidden directories (I believe in Finder it's 'Command + Shift + Period (.)' to toggle hidden files' visibility).
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