I figured out a simple hack that mostly fixes this problem. I put all of my hidden pages behind a parent page I call Hide Page, then I hid the Hide Page from navigation. Not perfect, but if the plug in fails again I only have to re-hide one page.
I am having the same problem. It has now occurred twice. Is there a fix? Does anyone know of another plug in that accomplishes this? I am no power user and don’t want to mess with lines of code if I can avoid it. I have hundreds of pages and cannot deal with resetting them every few weeks. It seems to occur after I add a new excluded page.