Board Thread:Lore Discussion/@comment-69.34.43.119-20140525201439/@comment-75.75.80.173-20140611045236

Pelinal Whitestrake wrote: Jyggalag hasn't got anything to do with the disappearence of the Dwemer. As far as we know about the Dwemer, I suppose not, but we hardly know anything of them. We only know that the Numidium and the Heart of Lorkhan are connected to their disappearance.

Jyggalag had "disappeared" for a long time as well, and being considered the Daedric Prince of Order  ( & being mistrusted by other Daedra ), he would be the most likely Daedra the Dwemer would even tolerate. It is really just a theory.