That's interesting... you mean like an AR code? I didn't realize that there was one, though I guess I should have assumed.
If you haven't infected them all yet then just try it with one—if you have then I guess it's not a big deal. I'm wondering if the AR code automatically gives the 'default strain' of pokerus, which although technically legit may look suspicious. I'll check it on pokecheck whenever I get one of them back.
If so, I can trade you a pokemon with a non-default strain that you can use to infect manually and will look more legit.