Shelves are the same as Collections
The term used by Kobo changed and frankly some if use the terms interchangeably. @jswolf however will attempt to remind everyone to use only Collections .
Now unfortunately if calibre doesn't show the books as being on the Kobo calibre won't be able to perform collection management
so let's see if that issue can be resolved.
Firstly, let's run calibre in debug mode, connect the Kobo, eject the Kobo and then post the debug mode that will be displayed. Among other things it will show us the version of calibre and any plugins you're using
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