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Many thanks for that. Moving them out of the koboExtStorage directory, and putting them into different directories below \root did the trick. Simply doing it with Windows explorer was enough, Calibre wasn't required.
Many thanks to a fellow Kiwi!
I do think it's a bit of an odd design choice, and highly counterintuitive, that when you put an SD card in the reader creates a clearly labelled koboExtStorage directory. Logically that's where files for the reader should be placed, when in fact it's the one place you *shouldn't* put any ebooks if you want them to be detected. Plus, there was nothing in the manual about that.
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