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What the plugin was doing in earlier versions wasn't really "duplicate checking". All it did when you chose the "Add to shelf" option was looking to see if the goodreads id that your calibre book is linked to was already on the shelf, and warning you in the dialog. Since there is no harm in putting the same goodreads id on the same shelf multiple times I removed that functionality to speed up adding to shelves with v1.6.
True duplicate checking would be comparing title/authors, not goodreads id. Goodreads already have that functionality on their website as a feature they offer for your shelves. In addition, if you were using the "Sync from shelves" feature of this plugin, you could setup a sync action to set some tag or custom column to show you that a book is on a particular shelf. So by then searching within calibre you could tell what books were on what shelves.
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