Correction: use ur 5 other units than the banned one. Unless youre doing the seed swap.
But yeah replacing MoBo, does fix it. so long as its cfw able so you could use your SD with you games and stuffs.
Id rather get a new console to be sure cause ninty may be able to counter that seed fix.
On another note, dont you think the save file plays a part? say you did seed swap. Then u go online, server thinks "hold on, this trainer with this TID and SID and HID, went on few days ago and got banned and now hes on again. check the hashes, cross reference, reban the new seed" (just plain thought)