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In Fullmetal Alchemist (manga and Brotherhood), there was a time where Al learned from Barry, before the battle with Lust, that a body could reject a soul. Hawkeye and Al arrived to where Barry was standing over his own (supposedly) dead body, and said:

It seems a body can't hold up with another person's soul inside it.

... Which worried Al enough to start thinking about how long he has left in his armor body. The thing that seemed to be overlooked is that after the fight with Lust, Barry's human body got back up and erased the seal to kill the soul and the body. So, it seems the body didn't reject the soul.

Also, in the next episode/part, Al spoke of the body that he and Ed transmuted in their basement rejecting his soul when it was transmuted into it. But that wouldn't be so much a rejection as the body being unfit to sustain life.

So the question is just that: Was body rejection ever really a threat for Alphonse, or any other person with a soul fused elsewhere?

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I think that yes, body rejection was possible, but we only ended up seeing situations where it hadn't happened.

Barry was number 65 (or something). I think it's possible some of the other 64 failed in their soul transpositions.

We did see Al loose consciousness a couple times - I assume that's when his armour was rejecting his soul.

I think that Alphonse was protected by plot, though.

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