Fantomas wrote: He talks about remembering though, just before Clara speaks to him: "But I can remember, Clara. You don't understand. I can remember it all. Every time... and you'll still be gone. Whatever I do... you still won't be there."
I wouldn't take that quote literally. I doubt even the Doctor is capable of holding two billion years' worth of memories. One interpretation of "I remember it all" is that he's talking about the time he spent with Clara. He's despairing at the realization that no matter how many times he goes through the cycle, Clara will still be dead.