Basically the whole thing started as a sort of what-if Ed accidentally opened the gate (by doing clappy alchemy) before he realized he could *do* clappy alchemy. He accidentally opened it to it's AU destination of the GW verse, where he lived for - well, I could be wrong, but I think it's two years. When he returned to the other side of the gate, he gave his memories in exchange for regaining time on the other side of the gate. When he re-enters the opposite side of the gate a la the end of 51, he will regain those memories but lose two years time - i.e. Kip / Duo will age four years while Ed / Solo is gone, so that ultimately, they're the same age.

... you would not believe how long that took us to figure out! XD