It is obviously quite easy to "Exit" KOReader, and KOReader allows you to browse book files and a long-press on a book's listing will allow you to Delete the file, along with other options. The problems you seem to be talking about sound like they are with the stock software and the Nickel user interface. As far as I know, though the Nickel interface doesn't have a file manager/browser that would let you see the file structure and give you access to /mnt/onboard/. If you connect your device to your PC it can look at the file structure of the device and use your PC to manipulate the files.
Luck;
Ken
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