I think Karlach was simply sold into slavery, no soul involved. Also, in the cut endings with Withers, her soul / spirit joins the companions gathering 6 months after endgame.
Yet the former
who is able to bring back her spirit from the Fugue Plane or where it ends up back the Material
who resurrects you after Bhaal kills you
is unable to bring her back...
Solid plot/conclusion through and through, lol.