How would I know, as you are not providing a save. As you can see from the quote you quote, the only problem that can happen with Lucy and MC room first time is if you been using a mod, save-editing or a bug itself in the game. If you are not using any mods then maybe it is an unforeseen/unknown bug somewhere in the game. However, I am unable to see any bug in the game and highly doubt it is a bug. Reason for this is because the problem cannot happen before doing house missions; so how can you get this bug when your now come to the new house. Hence suggesting the user is using a modded save or mods. This is why I ask and assume that. Only if you provide your save, I can confirm as with HotPipe save.
Can be fixed two ways:
Try creating a new save, then when in-game, load the save that is giving you trouble. It should load, then you can re-save.
OR
backup saves ONLY, not config or global, delete everything in the save folder and start a new game. Save at the slot that are the same as your backup. Copy back your backup and overwrite your new save. They should now load up fine.