These would be my suggestions.
The easiest (a9lh) option is to simply use another SD card. Stick it in the 3DS and let the system initialise it, then copy the the arm9loadhax.bin to the root of you're SD card and you're set.
After the tournament stick your other SD back in.
or
Back up your NAND and SD card then remove all suspect titles or restore an old unmodified/prehax NAND dump. After the tournament restore your CFW NAND dump.
or
If you have a9lh installed, set up a fresh emuNAND, update it and have luma3DS boot directly into it instead of sysNAND. If you don't mind the space it takes up you can leave the "clean" emuNAND partition for future events, or delete the partition post tournament.