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How does it work if you cast Lightning Bolt through a square with an invisible enemy?
It hits them and they have to make a reflex save.
A lightning bolt has a line of effect, but that line is still an AoE (it's just in the shape of a line instead of a sphere). Anybody in the AoE gets hit, whether you can see them or not.
I Agree with MisterSlanky, same as with Fireball or other AoE Spells.
Ironically, that very question was used as an example HERE just the other day.
R.