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Is this on your computer in calibre's library view or on your Kobo in My Books => Books? If this is in calibre's view, I've never seen it show a 0, just the checkmark/location/copy count being removed from the On device column if all copies were deleted. If on your Kobo, I've never seen a book show a count of the number of copies on a Kobo. If you remove a Kobo purchased and synced book, it will change to showing as being downloadable.
Perhaps you could attach a screenshot of calibre or your Kobo so we can see exactly what you are seeing.
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