Just thought up this theory and wondering if any1 agrees. Its said very clear that the dwemer were elves and would be related to members in the psijic order and it's also said that they share a power where you can communicate between a person in silence (college of winter hold storyline when a member talks to the dragon born). So with the dwemer and members of the psijic order are equally as powerful as each other. But maybe, the disappearance of the dwemer was caused by the order. Maybe the dwemer had a breakthrough and wielded a power similar to the gods and thus defined the psijic orders beliefs and so the order banished the dwemer to a plane. During the long time in this plane where the dwemer live forever, they finally manage to rebuild this great power they discovered before, so the psijic order teleported their hq to this plane in order to keep the dwemer from escaping. The plane which they are held time goes on endlessly and so anything inside is immortal explaining why the psijic order is still going.
So in short the idea is that the Dwemer were deemed "too powerful" and like with the Eye of Magnus, the Psijic's removed them? (I want to be sure that's the overall point). I don't remember reading any Dwemer were members of the order, or related to any, do you have info on that? All that aside, I believe it's established that using the Heart, Sunder, and Keening the dwemer disappeared, not through the actions of any other outside influance. From there is where the theories very.
The Dwemer became the Oversoul of Numidium, their crowning achievement. This was always their goal, although the end-product was more faulty than they would have liked. See the Final Report to Trebonius.
There is quest in Skyrim that shows how they disappered,more or less.You will have to get 10 dwemer cogs,a warped soul gem,and do something with the gem,then you wait 10 days and talk to the person that gave the quest again (Arniel).Then he will send you to get Keening.Then he gets surprised you didn't died and then attacks the soul gem in a pedestal,after some hits you gain a new spell and he desappear!The dwemer had more power,so they turned into like,Daedra!But not so Daedra,they just turned into weak gods,i guess