The logic could be that if you have it on your wishlist and then download a preview, if you then delete the preview it means you are no longer interested in the book. But, from looking at the database, I suspect that they are simply deleting all record of book when the preview is deleted.
I agree about the Kobo desktop app. It should do more management. At the least it should list all books like the "Purchased" list on the site. That way the book can be marked to put onto the device at the next sync or not. Being able to mark books to go to a particular device would also be good.
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