HonoreDB comments on Harry Potter and the Methods of Rationality discussion thread, part 5 - Less Wrong
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How did Sirius manage to switch with Peter?
With Harry thinking the best way to break out of Askaban not to be sent there in the first place when he first hears about Sirius, the Quibbler story that Sirius and Peter are secretly the same person and someone Fawkes is particularly unwilling to leave in their Askaban prison cell mumbling "I'm not Sirius" over and over I have very little doubt that it somehow happened. I see no way to show that all just to have been a red herring that's even the least bit awesome. And then it has also repeatedly been mentioned that there seems to have been no reason for Sirus to search out Peter on that day and been made abundantly clear that those events did not transpire as in canon.
So how did he manage it?
Just forcing Polyjuice down Peter's throat doesn't seem like it would be enough since it's limited to one hour. Maybe Peter is a metamorphmagus (or human-form animagus or something) and Sirius imperiused or otherwise mode-locked him? If there was a way to trade bodies I think it would have been hinted at by now.
I made the same argument on tvtropes independently. My thought was that Sirius and Peter were human-form animagi of each other, as a wizardry analogue to getting matching tattoos. Although maybe one's choice of animagus form is involuntary: Peter was completely obsessed with Sirius at the time that the two performed the spell, but not Sirius with Peter, so Peter's form was Sirius but Sirius, to his surprise, turned into a dog instead. Maybe that's why they broke up.
I'm not sure the dementors see people the way we do: they certainly don't in canon. If Peter's mode-lock wore off in Azkaban, the dementors might not notice or care.
If Fawkes thinks that Peter is innocent, he probably is. But maybe Sirius is too. Maybe Sirius was the only one who knew that Peter was the secret-keeper, so he assumed that Peter betrayed the Potters but he'd never be able to prove it. So he switched identities and faked his own death, and remains ignorant to this day that Voldemort doesn't need a traitor to find his victims.