Action Replay can mess up your game by corrupting save files so they can't be accessed. basically you have to start a new game. or they can work just fine.
it all depends on the code in question because of what an AR actually does. Pokemon uses a hexidecimal system for its programming. so an AR changes the hex code of something to something else. usually you get more problems when you make drastic hex changes, like changing a Ninjasks ability to No Guard and teaching it Sheer Cold, as opposed to just teaching a Pokemon a move via TM that is normally only an Egg Move or Tutor Move. its hard to say 100% how the code in question will affect the game, since not too many people know the entire Hexidecimal spread for any given Pokemon game. hope that helps.