Then again, if you run out of VP in a 2-player-game, I suspect you're playing it wrong.
Agreed. Having played this as a 2,3 and 4 player on a number of occasions I can't see how it could be possible to run out of vp chits. For the sake of argument though I would say that Jens is correct, each return 20 vp to the pool and add it back to your score at end. Or each have a secret score pad, total points at the end of each round and return all vp to the pool.
What have your scores been? Our two player games typically end up between 75-100, including hidden role bonus points.