I already made a skyrim fan fic, but when I went into that story, I was improvising. Now, while I'm a wonderful improv actor(courtesy of playing pretend games), but that was past my skill.
The young dwemer looked at the project they were currently working on. A way to create a soul. It would take thousands of years after they were dead and gone, but it would be worth it! The soul would slowly form inside a metal suit the size of a normal Dunmer, for that is what they had decided to use. Dunmer blood, to create a Dunmer soul. They had installed an extremely high tech voice box, along with other metal organs. It would seem completely normal, but it wasn't. They would be ready to form the soul soon.
"Alright everyone!" Grulen Tagrenz, leader of the project, said, "Time to start add the blood!" They had used a variety of other ingredients. Blood was just the final one. Dremzlin Tagrenz, Grulen's daughter, came over with a large bowl of blood. She handed it to Grulens and backed away. Grulens looked at it and took out a soul extractor. He looked at it. It contained 1/4 of his dead son's soul. His son had died from a centurion malfunction. That had been happening to all the automatons as of late. His son had just been unlucky enough to be the nearest target for the centurion. Grulen had been just quick enough to take some of his sons soul, most likely the lesser part of the mind.
Grulen imbued the blood with the liquefied soul. He placed the mixture into the chest of the machine, with the rest of the ingredients. He closed the circular hole and sealed it, then turned around and looked at his colleagues. He noticed them dropping to the ground before disappearing, and he felt their presences leaving quicker than they should be. Suddenly, he felt quite faint. He dropped, and his soul raised up from his body. Instead of going to Aetherius, it went into a soul gem, specifically the Heart of Lokhan.
I went with a different lore than they 'just disappeared!'