Yeah that's what confused me, did he mean he got the skill from her soul, or from fighting her? Because he pretty much learnt how to use the piano during her fight.
I may not have read it all properly but the soul that soul ate to become a death scythe (the witches soul) belonged to Arachne, now I might not understand soul eater but everytime something dies it leaves its soul... if her soul was left behind then I think you can assume she is dead...