When I originally started planning Elibian Nights, I decided to cut several characters from the cast. They'd have cameo appearances, perhaps, but no major story roles. In the initial drafts, Bartre and Karla were confined to a house scene in Lyn's Tale, Dart was only referred to by Fargus, and Nino and Jaffar were completely missing.
I didn't really much care about their fates, and had no interest in chronicling it. However, as the project grew, it eventually encompassed the entire cast. It came to the point where Jaffar and Nino were the only characters (save Athos, who had died) that didn't have a story role. So, Jaffar and Nino were reunited in the second part of Pent's Tale, and that fulfilled my duty to somehow incorporate every member of the FE7 cast. I'll admit it, they were initially simply thrown into that tale because they needed to appear somewhere. That tale needed a few more playable characters, so I made it work.
Obligation fulfilled. I'm done. No more Nino and Jaffar....right? Well, that's where I was wrong. When I started brainstorming for the bonus content scenes, one of the first ideas was writing the meeting between Lucius and Nino, where Nino left her two children, Lugh and Lleu, as orphans in Araphen. So heck, I did it. Why not?
However, even with the minor appearances by the two, somehow the story feels more complete. After FE7, the two lived happily together for a time. Nino grew into an adult, and she and Jaffar were married. However, bounty hunters, having learned of the "Angel of Death"'s whereabouts, began to appear. Jaffar, wanting to protect Nino, believed that being near him put Nino in danger, and that if he left then she could live the rest of her life without worry. One morning, Nino awoke to discover that Jaffar had left. Unable to live without her lover, Nino began her journey to find Jaffar. The two would eventually be reunited in Reglay Manse, as Nino stopped Jaffar from assassinating Lord Pent.
After the events in Reglay, Nino and Jaffar settled down together once again, this time in Pherae under Eliwood's protection. Nino became a mother of two twin boys, and they lived peacefully . . . for a while. However, even Eliwood's guardianship couldn't keep the glory-seeking assassins at bay. Jaffar couldn't stand to put his wife and his two children at risk. He vanished once again. Nino, as she did before, embarked on another quest to find her lover. She left her children in Lucius' care, and promised to see them again once she found their father, and the four would live once again, a happy family.
However, that day would never come. We know from FE6 that Lugh and Raigh were raised as orphans, meaning that Nino never returned. What happened? That's where you still get to fill in the blanks with your own personal headcannon. My personal preference - something that I'd considered doing in Elibian Nights - was to replace the first Cyclops fight in Karel's tale and turn that into a match with the Angel of Death. Of course Karel would be part of the hunt. Nino, having just reunited with Jaffar after searching for him post-Tale 4x, would stand with him and get slaughtered by Karel. It was deemed a bit too cruel to publish, even by my GRRMian standards (see: Raven's Tale).
Nino and Jaffar went from "cut characters," to having their tale almost entirely told. The cutting of Jaffar's death was intended to leave the ending vague, and leave the story of Nino and Jaffar unfinished, up to the imagination of the beholder.