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Well if its just to get an FC I doubt you will lose any data, I don't see how that may effect another game that has a different FC ;). But if you want to take caution do some transfers.
Whoops nvm just saw your message after posting my reply. Hm well it seems safe to me, but you may want to confirm this in a help thread here =/. Or you could just see if someone reliable here can help you do some transfers to PLAT.
The Azmuraill was nicked? T_____________T well I think the other I was trading for is not the same as the one you have :P, but hey you still get a GW pikachu free ;3.