One hour later, I am re-evaluating my estimate. Now it should be available in about a half hour. xD
I'm afraid I really can't provide any in-depth details on how this issue came about - I don't know myself.
I was playing on my Witch Doctor, up until the point where I entered the Ancient Waterway. I figured I'd take a break from the game for a bit, so I 'ported to town, and exited the game. Upon logging back in and resuming play (from the latest checkpoint - the entryway in the Ancient Waterway), I saw I had two instances of Zoltun Kulle with me.
I talk with them both to show off that they are both "interact-able."
The majority of the video is me just playing on...seeing if the issue will resolve itself, perhaps when I zone into another level of the dungeon, or whatever.
When I get to the point where I break Shen out of the barrel, Shen replaces one of the instances of Zoltun Kulle. This remains the case up until he "leaves" your party when you encounter Gavin by the cursed relic - then I have two Zoltun's with me again.
Anyway, tl;dr, it didn't go away on it's own, over time. After finishing and exiting the Waterway, I logged out and back in. Once back in, I only had one Zoltun Kulle with me.