Alright, this was Heart Gold, I already beat the game. All I wanted to do was battle my friend Keenan and win, yet he trained like 10 level 100's within a week. I trained one in a month. Basically I just used the AR for the berries that reset EV'S and the pokemon modifier so I could battle any pokemon for the effort values I desired. I know it may seem lame, but I just wanted my team to be able to take him on. Anywho, what is affected in my game is the pokemon day care. I was breeding the other day for the first time in ages because I had a brave scizor (I wanted an adamant one) so I ended up getting the egg from the old dude, and after cycling up and down golden rod for half an hour I knew something was wrong. The egg's status didn't change at all. I managed to delete it with another code, yet alas...no luck. I'm just going to go and get another copy and not use an AR this time. I have searched everywhere on the internet and pretty much everyone is saying that this could be permanent. Thanks anyway for all of your responses.
I forgot to mention...I saved with the egg. I kept trying to breed after I deleted that one, but even after dozens of eggs, none of them would hatch.