They did switch souls. It's not clear what happened to Hecate or Circe's soul - of all Perez' Claremont moments, the Circe thing was the worst - but Circe believes that Hecate will somehow return and take her soul back and that will be the end of Circe, which suggests that Circe's original soul is irrecoverable. It makes the most sense to assume it was simply destroyed.