Hmm, I thought he disappeared after disenchanting the heart? Though I can't see how he could've been truly killed, in the mortal sense of the word, if he was at The Trial of Vivec -- which, AFAIK, is considered canon?
Are you talking about Vivec or Dagoth Ur?
Neither disappears after disenchanting the Heart. Dagoth Ur usually falls in the lava, but that's not supposed to happen, you're supposed to finish off his non-deified state after removing the Heart. His death animation is the same on that he has when you kill him the first time, which coupled with the fact that Vivec himself states afterward that he isn't even sure if Ur is truly dead, and coupled again with the fact that Ur was already dead anyway, and it makes you wonder just how much you accomplished.