When you link a chapter to another, it creates a new chapter that's invisible to the reader. If I set the invisible chapter to change variables, will it change them or is the variable change skipped because the viewer doesn't actually see that page? The reason I ask is because I couldn't find an answer to this anywhere in the FAQ and when viewing the story myself, the chapters that are invisible for the viewer are still visible for me, so I wasn't sure of how it would work in practice.
Well, there is no "invisible" chapter. If you click a linking chapter, it will be opened and processed. - If you are the author, it will be shown and you can use the link to reach the link destination which will be processed as well. - If you have no editing rights, it opens the destination chapter automatically which will be processed as well. (So both chapters' Score Changes apply.)