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Since you already have KOReader installed, you might consider putting your "sideloaded" books behind a "hidden" folder, so that you won't have to worry about Nickel's database issues. A hidden folder/file is one that has a name that begins with a dot/period, like: ".books". (You can make hidden folders by naming them with a dot on both ends, like ".library." which windows will drop the trailing dot, leaving you with the ".library" hidden folder you want. Any files or folders you put into your hidden folder will also be hidden from Nickel's processing.)
Luck;
Ken
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