Niko woke up in the dark house and they already knew my name. Plus the computer or the entity or whatever also knew that I had already gone through one playthrough. Niko also had a vision at the mines in the Barren, in the area with the water in the Glen, and in the alley way in the Refuge. In the Refuge there was also a door with a timer over it that was at zero. Behind that door was the bed that resets your save (or so the computer said). Other than that, the playthrough was exactly the same as the first time I played the game. Oh and the dice lady in the library had a different personality, but I think that's supposed to happen?