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pretty sure its wasted, i did the same thing for that blond wizard at the beginning and now she is one point skill point short compare to another wizard of mine. if you wonder why i have a generic wizard, thats because these main story characters are just...weak, no head wears, even their specialized weapons are weak compare to the games best weapons, not to mention cant change class
It's not wasted. Never. You either used it accidentally or... idk, there's no other way it can disappear. I know because I kept skill points for several characters to use them on later skills, including the story characters.