User blog comment:Miskos3/Fairy Tail Chapter 374: Revolution, Review/@comment-5303512-20140307135954/@comment-7418318-20140307155444

Apart from what Miskos said, I also have some other possible ways ready:
 * Hades got his hands on the Demon Heart he used by selling his soul. If so, his soul would be bound to the Demons and go to them after his body dies.
 * When FT fought Hades, he was already missing part or all of his soul, since he had traded it away to the Demons.
 * Zeref might have stolen Hades' soul when he killed him. He might have given it to Fran directly, or Franmalth has access to the place it was stored and just took it.
 * Hades might have lingered as a ghost (like Mavis or Roubaul) and Franmalth absorbed him that way.