Hello! Thank you for letting me know - I discovered where the issue is, and just pushed a fix!
Bad news is, there is a chance that if you were playing an earlier save, you might have to play from the beginning of Chapter 3 to get the broken flags fixed :( I did, however, leave a shortcut to the spot where the Null Path occurred, so if it occurs again, clicking on the shortcut and playing from there should fix the flags!
Good news is... Weylin's route has been broken for some time at that exact spot, and thanks to your error message, I finally discovered where the error was. So thank you a lot, it should work now <3