In the past, Safari Bookshelf subscriptions were based on a total number of slots used, not the total number of books in your Custom Collection. This was changed so that now all books only cost 1 slot.
Safari allows you to swap books in the Custom Collection in a process explained in section 8.0. The only rule is that a book must remain in the Custom Collection for thirty days before you can swap it for a new book. Also, you can upgrade your subscription to more slots as the need arises.