Well as I said before I had no issues with an almost complete previous version of this same game and haven't had this problem with any of hundreds of others of games of various types. It's unique to this particular game. But I'll indulge you and move it to its own folder on the drive it's on when I have time later to see if that changes anything.
EDIT: Uninstalled and reinstalled on a folder directly off the drive, loaded up the save from a backup and still have the same problem in the same spot. Still able to play through other routes (again, for now, haven't had time to complete their routes to test). I don't have time at the moment to start a new game completely from scratch to test since it takes a long while to get to the mother path that starts breaking for me, but I suspect it wouldn't change anything.
I'm aware. The first game of this type I ever downloaded 10-15 years ago was an Illusion game so after that I pretty much just kept all of these in that same subfolder since it was easy to remember. Ren'py, Daz, HTML, "Other", etc.. Just easier for me to keep track of and keep the folders cleaned up when I complete the games.