By only playing the most recent updates you have, effectively, navigated your game deftly dodging scenario fixes EK has retro-actively put in it.
Python:
# CHAPTER 12 PART 2
label chapter_twelve2:
//...
if holly_ivy and lena_go_holly > 3:
$ lena_go_holly = 3
This bit would ensure to switch off the trinity route for Holly who is under Ivy's influence, if you replayed your game from before you get Lena's POV in Ch.12
So yeah, you have a bugged save, and while you're reaping the benefits, there's no telling when/if this backfires and your game goes all ¯\_(ツ)_/¯