That's a good one. No idea then as I don't use Scrappy's mod on most of my games. I prefer not to replace game files as anything funky can and does happen. Especially on a game with code as complex as BaD.Whatever path I choose, by episode 9 whenever you can check which girls you have been with on the phone, it will show that I took part in the scene with the fj where you go to the closet with Sarah afterwards. I am using Scrappy mod on all seasons.
If the mod has a thread here, I'd check there to see if it's a known bug? Otherwise someone that uses it would have to provide more info. Not something I remember seeing on the unmodded game, but I'll double check when I'm at my desktop later.