After going Bajorian Jesus and giving a prophecy of his return, he'll show up in the novels in the form of dream visions and Orb experiences for awhile. Jake goes into the wormhole searching for him but even though he feels his father's presence, he never finds him.
He does make good on returning though when his second child is born. After that he's just on Bajor living with his family. He'll return to DS9 eventually to help out during a crisis once though. Otherwise he just pops up now and again, attending a baseball game on Cestus, and working more in B'hala.
He briefly returns to Starfleet during a crisis, only to resign, return again. He's sorta lost for awhile feeling abandoned by the Prophets. His dad dying while he's away doesn't help matters. He divorces Kassidy to protect her, since trouble always seems drawn to him.
He's really a lot more distant and cold after his return from the Temple, and a lot of the crisises that the Federation goes through compound that. Really his story in the books isn't happy at all.