What happens is that calibre will ensure the records are marked as deleted in the database on your device, then, when the next sync is done with Kobo the records will be dropped from your device AND marked on the server side as being deleted.
If you're at all comfortable with using SQL tools then it is also possible to modify the database yourself and have similar effects to using calibre.
PS: It has been suggested to Kobo dev's that adding a function to clean up these duplicated shelves to Kobo Desktop would be a very sensible idea.
Last edited by PeterT; 12-27-2014 at 09:56 AM.
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