I would think that if something did happen from the glitches and stuff, the Pokemon would've been deleted... I've had that happen, but not through cloning.
Actually, now that I think about it... if the cloning method glitched up, the Charizard might look odd on Emerald, yes, but once it's Pal Parked, there really shouldn't have been any visible flaws. It would just say Hoenn, Arrived at yada yada.
Just another fishy bit to add to the evidence, I guess.
It seems like you're pretty bent on the trust issue. Coming from a neutral person, I'd say they're not telling the truth about how they got it... just taking it from the facts given, really. This wouldn't be the first time someone gained someone's trust and tossed it aside in history, ya know~
That's up to you whether you think they messed with you or not, but either way that Zard's status is hacked, haha... badly at that. I'd release it. This is all I can really say for now.