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What if the new immune system had somehow 'assimilated' the rest of the original body into its, for lack of a better word, jurisdiction? Because, otherwise, wouldn't every organ in the girl's body come directly under attack?
Maybe the immune system can somehow identify genetic similarities between all the organs and, this is where it gets scary, deduce from that evidence that they all belong to the same organism, and therefore don't need to be purged?
OK, so it makes no sense and has no medical precedent to back it up. But SOMETHING weird happened in that girl's body, why not go the whole nine yards when making the hypothesis.
the end of all disease? find the one person who has immunity beyond measure, clone his liver and ta-daa! everyone can be fixed.one day...