Hey, I just wanted to share one info for other gamers who may also get their saves corrupted like I did. At some point I was surprised that Lily is missing. She was not appearing in her room. Only very few scenes featured her from time to time. Looks like for some reason she was gone from all locations and some usual script that made here appear in her bedroom didn't work. From time to time, a breakfast scene with her got broken (stacktrace appeared).
Through findings of all_people_in_the_game() function and fact that major locations are named very conveniently, I managed to call following to get Lily back: lily_bedroom.add_person(lily). I have called it right before breakfast scene that was breaking. I'm not sure if it is the right time. Maybe you can also do the same in the usual times when she is in her room (early morning, night).