I completed my playthroughs and didn't see any damage. I believe damage happens when you use a code that tampers too much with the game like walk through walls or something like that. I've even caught Missingnos in my games with no damage (despite horror stories, lol).
Anyway, I ask you another completely unrelated thing. We have two months until XY release. Do you think it's worth it to try and fill my Pokédex in Black 2? I really want to do it because of the Shiny Charm, but I'm not sure it'll be worth it. I don't have access to event Pokémon. I can download events from ProjectPokémon site, but I'd like to try and keep it legit instead. I also don't have much to bargain with, since I restarted my Black game which had a few goodies and stupidly forgot to back them up.
I don't think it works that way. Once damage is done, its done. If you have no issues you should be in the green, just don't push it any further than you already have. You still have to abuse the use to get any heavy damage.
I'd also like to warn you about PokeGen. The Pokemon Company and Nintendo do not endorse the product and have issued warnings that it will corrupt your game if used. Please use caution if you use it. They will not reimburse you for any lose to your game.
Did they? I mean, as in an official statement?
I know AR can tamper with the games but generally only if you're very careless with codes...