In Pokèmon Sun, I got my Shedninja via Pokebank, but it wouldn’t listen to me! It is level 100 and I have all the level stamps. (My level 100 Silvally listens)
I don't know. I know you might not want to do this, but breed another Nincada and evolve it and level up. That's all I can tell you that I am sure will work. Maybe hmmm, you can try trading it with a friend and trade it back? No, that sounds silly. Try beating the Elite Four again?