I wouldn't be surprised if there was some Pokemon that could reverse time like that. In that case I'm pretty sure you could be made to..."ungrow" and forget everything you learned or knew in Johto once you return to your world.

Sorry, but I don't think there's a straightforward answer for what's going on here. It's really impractical to put your faith in that idea, I know, but you sort of have to muster up a lot of faith in this world.