I have had a similar problem. Not sure about completed quests as I have never gone back to check them. However, mine seem to disappear when I go to solstheim. Mainly the misc quests. they are still active because if I do one of the objectives the quest will reappear. I went back to a previous save and wrote down the ones that had vanished then continued on. On this playthrough I have not been to solstheim yet but I hate the thought of going because I have so many open quests. I doubt this helped any but just know you are not alone.
