Shadow Crystal in Chapter 2
So, you defeated the secret boss of Chapter 2 and got his shadow crystal, then you went back to the castle and the shopkeeper told me you could get the one from Jevil’s if you defeated him.
How does that work?
You can go back and simply do the encounter.
Once you have the item the game will know and upon checking that little hole in the wall on the left most part of the castle town the item will be inside it.