Well, I'd give the two methods outlined above a couple of tries before giving up on it entirely - it's a lot to lose, after all. If you DO manage to get it to work...buy a Pokemon Bank license and transfer everything you value onto there.
I'm not sure if Nintendo would offer this for your region - I have no idea where you are, haha - but if you can't get anything to work you could send it to them to see if they can repair it; they may or may not be able to get the game to work. Didn't help me at all (they tried to charge me full RRP for a new copy!) but...eh, different circumstances since your game is still registering, and if you can't get it to work yourself then it may be worth considering. Good luck!