whoa, whoa, whoa. hang on. it went like this:
hohenheim walks through the human transmutation gate. he disappears from amestria and is known to exist in some form in london.
ed walks through the human transmutation gate. he disappears from amestria and reappears inside alter!ed in london. when alter!ed dies, ed is returned to the gate and walks through it back to amestria.
presumption: the hohenheim we see in london is hohenheim elric inside of alter!hohenheim.
conclusion: when alter!hohenheim dies in seeming noble sacrifice in munich, hohenheim elric returns to the gate and could walk out of it into amestria.
reaction: well, fuck!
the italics, they kill me ded.
eta: of course, it could be that since the original alter!hohenheim wasn't an alchemist, he died a natural death three hundred and some years ago, and hohenheim has to use his own body when he goes though. this is suggested by the way hohenheim in london seems to have the same gold-colored eyes, while alter!ed's look more hazel.