Yeah i was wrong about the rat affinity skill, it was given and then you were given am option that would lead to a bad end, so it definitely would make semse that skills developed while on the run with Pyrrhus werent carried over since it all took place within the choice-zone of the reset. Still, im very interested in how you think the errors and resets work in-universe, its such an interesting mechanic that could either have no effect on the story or a massive effect on it. Because of the meta nature of the game both im general and in universe since the MC knows this world isnt exactly 'real' it could be really cool if the MC became aware of the resets and started doing things on purpose that causes them, especially with the introduction of the amorality skill in Pyrrhus' last route, you could have MC purposefully start doing really dark things that will force a reset in order to gather more skills, and have a concurrently running storyline where not much is different except internally MC is slowly becoming more and more dark from abusing people and things in these self created error timelines.
Sorry that was just a lot of rambling XD im really enjoying this game exactly how youre making it so you dont even have to consider my weird ideas haha, keep up the great work!