Okay, I think I finally figured out what's the issue here: if I give players choices, but then use a script to hide them all (if, for example, they don't have any of the necessary items like in the case of the medals) the game doesn't like it (maybe the engine is still waiting for you to pick a choice that is never going to happen). Now, this specific instance is easily fixed, but there might be more in the game, since I didn't know this was a problem.
I'll fix this, but I don't now if I can track down all the other instances, hopefully it won't eat too much time.
. Definitely a shitty thing to discover late in development. I wish I could be of more help and remember where else I encountered the problem. Last time it happened to me was a year ago. By the time I realised what was happening I had deleted all my saves at the time and was never able to reproduce it. Thankfully when I saw it again I was ready lol. I want to say it was before chapter 4 and not the same temple but I can't be sure.