Not a stupid question at all. In fact in doing some more testing now I found a bit of a problem with the whole tags/shelves thing, and it is to do with the Goodreads API call I am using.
To get what shelves a book is currently on, I am doing an API call which gets your "review" for a book. It is all horribly unintuitive, but as I understand it what happens is that if you add a book onto one of your shelves (I believe one of the "to-read", "read" or "currently-reading"exclusive shelves), then Goodreads will create a "review" record for you. It is then this review record that is retrieved by my plugin to identify the shelves a book is on.
If you delete the book completely on Goodreads (as I just did in testing) then Goodreads deletes your review record. So this means the plugin can have no information about what shelves the book is on.
Now I think that is a flaw, so I have just changed the logic so that you do not have to have a book on your exclusive shelves for it to live on another shelf. I will update a new release in a few seconds...