The box is still in the car. If you unscrew the intake and lift it up, you'll see that the box is a separate piece. Tape over the opening of the box as well as the other tube that comes off the intake. Thats all I did. Make sure the tape is not visible and vola... no warrenty issues.
Nothing complicated and the system is all intact... just air doesnt flow in and out of the silencers.
Hope that helps.