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I was thinking of giving that entire section a giant nerf and having it only happen on New Game+ runs. But, while such a patch is brewing, there are no dramatic repercussions of running into such scenes in the story. For 99.9% of the game, it's just flavor text to make one's run more unique. I'm afraid if you delete the persistent files that keeps track of such decisions, the script will create a new file that says you did that and add an entirely different set of flavor text.