The Kids Are Alright (1) - S6-E1
Plot hole: When Joey walks into her class and sits down, her cell phone rings and her Professor answers it. As he listens to Audrey on the other end, he says very quickly that he got the message. But when he relays the entire message to Joey after he hangs up, the message is much longer. There is no way he could have possibly gotten that long a message in the very short time he was talking to Audrey and said 'he got it'.
Answer: It's the same apartment Joey had in NYC. Comparing it to the beginning of the Finale; you can tell it's exactly the same location, furnishings, Plasma TV etc. Apparently Chris was only living with her at HER apartment, and now Pacey has taken his place at the end. I guess this implies Pacey successfully started his own restaurant business in NYC as he had dreamed, to be with Joey.