the boss on mana valley will die if you didn't closed the dialogue "pressing x". just press z or skip.
and if in that case it didn't work, deactivate the hack before you reach the final/boss stage. or deactivate the hack after you got your quest items then leave the dungeon (dont forget to deactivate it before leaving).
PS: you dont need to deactivate the hack immediately after the boss died, deactivate it after you get the items.