The files that made up that third copy are simply removed from your pool drives. They no longer exist. Each copy in a set of mirrored files/folders are valid originals, each as good as the other. It doesn't matter which set Drivepool erases when you lower the duplication factor.
You could have a duplication factor of six, then lower it to two, and the extra four copies would simply be deleted from the pool. Duplicates removed in this way also free up pool space.
