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According to this wiki, Almalexia only has a health regeneration ability while in the temple. Is this definitely the case? I've tried jumping onto a high ledge with a Scroll of Icarian Flight in Sotha Sil's room and attacking her from there. It works, but I do so little damage that I can't tell whether her health is regenerating between attacks (I have very little in the way of ranged stuff that can hurt her at all). If it isn't regenerating, then I can kill her, it'll just take forever, which I think I'm okay with. Otherwise I'll have to revert to a save prior to entering the Clockwork City and do something else until I'm strong enough to fight her legitimately.

I used the dwarven darts from the centurian archers. They do 50 points of damage and I was able to stagger her as well. So she did not regenerate in my case, she just died.