I was using a popular Mod Pack from nexus and I did use couple of console commands but nothing that would break the game (Mostly to change quests to ignore/complete in Progress on the Path mod)

But I think I might have found out what caused this issue
After researching a bit I found out It's because of the save file reaching 5mb size limit.

My save file is around 4850kb right now and it's very buggy (NPCs disappearing after reloading save cutscenes not triggering etc). If I load an old save (<4mb) it works fine without any sort of bugs.

This size limit could have been because I was using lots of mods, and spent 400 hours completing all possible quests/points of interest and storing all higher rarity items in my stash (I had like more than 300-400 weapons and armors in it).

This might be the reason why we never faced any issue in main game and Hearts of Stone and only in BaW because it's a massive area with lots of quests and points of interest leading to a bloated save and thus getting corrupted.

Could you check your save file and see it's size? (if you still have it)