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Hello,
I have similar problems with my BeBooK Neo (= Onyx Boox 60) and made the same setup in the plug-in to send my books to the "MyBooks" directory again (they started to go on root, I didn't understand how).
The question is now on the oter way around: is there any way to tell calibre to scan my card starting from MyBooks and not from the root? I usually put on the root tmp directories with books or other docs that I don't want to handle with calibre (temporary stuff), but as soon as I connect the device calibre lists those books as on the card and not in the library. I would prefer to keep consistency only between the calibre library and the "MyBooks" sub-tree of the device.
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