I can't guarantee it will. What I can state is that the hack checking device only cares about what is in your Battle Box. That was stated by Mike Liesik.
Luigi08 said:If you hack correctly you wont get caught, its that simple
EDIT: Its been done before, even people who hacked incorrectly to the point at which it was obvious got through the hack checks
ISB said:Either way, it's illegal, and you will (most likely) get caught and disqualified. No questions asked.
Chariblaze said:I can't personally confirm it, but I can at least tell you that I highly doubt that it will be flagged, since you're not modifying any Pokemon (IV's and EV's and whatnot).