Well, it's still possible to do the conversion, but some things have to be taken into account, like the new Abilities, Moves, and Items, which would be handled on a case-by-case basis I guess. As for the met location, I'm a bit rusty on the details, but I think it's possible to just generate a new met location based on the target game... or else I think something along the lines of "Link Trade" would work, if that location exists in the GBA (which IIRC it does).
But like I said, I'm a bit rusty on the details.