The after-dark version would take you to the right just past the Ship and Fort, instead of through the pillaged burning village. You'd go behind the existing sets on a whole new track, where the maintenance bay is now, and the attraction would be completely new from that point to rejoining the existing track near the end. It would be dark and filled with skeleton cursed Pirates.
From what I understand, POTC would close for a brief time each day to effect the changeover, and when riders in the new after dark ride got to the ship and fort, the ship would be filled with skeleton Pirates instead of the human ones that are there now. Jim Hill Media had a complete breakdown of this a few months ago, if someone feels like finding the story on his site.
Most of the work can be done without closing the attraction, only the installation of the new track and the switvhing mechanism would require that, so it may be that it's already in production.
No news of it happening at WDW yet - let's hope it's wildly successful so they do install it there too.