Originally Posted by paolol
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.
Go to preferences -> plugins -> device interface plugins and choose the BOOX driver (I hope that is what is being used for your device). You will see at the bottom a line saying 'Comma separated list of directories ...'. Put MyBooks into that box. That will tell calibre (or at least should tell calibre) to look only in that folder and subfolders for books.
Note that the setting does not affect how books are stored on the card. If you want a particular folder to be used on the card, then that folder will need to be in the save template, and that means that the folder will also be used for main memory. Result: you have one extra folder in the hierarchy for main memory, but that shouldn't break anything.