Pretty sure it won't brick the 3Ds just by updating. In any case, you just erase the save data from cubic ninja, by pressing L+R+X+Y for about 5 to 10 seconds. And delete the boot file from the SD CARD. Also just so you know the exploit isn't installed on your 3ds, it's installed on the game card using the save data to boot the home brew launcher. Nothing is installed on the 3ds, except the activity log recording that your playing cubic ninja.