Jergal was never gone, he's been working for Myrkul, then Cyric and now for Kelemvor as scribe of the dead recording everything that dies since he passed most of his power to the Three. I'm not sure why he would be punished now for it either, considering how long ago that happened.
Also, he's pretty busy recording things, so I doubt the skeleton is him. The skeleton could be working for Jergal thought.
I didn't mean that he was fully "gone" and then "brought back" to "life". I just meant that he had been brought to Faerun to assist the party against the Dead Three. We don't know what has happened to Jergal as of the last couple of years. Perhaps he had been imprisoned some time after the Second Sundering (by another deity that recently "returned", Helm, perhaps).
I still believe that the skeleton is Jergal, or at least some sort of avatar, as BuckettMonkey said, there are many hints in the dialogue we have seen thus far.
Just speculation on my behalf, it is possible the skeletal being from the crypt is something else!
