Oops!
Donny you are right. I found the episode on Netflix (called "white Tulip", duh).
Dr. Bishop warns the time traveller, Peck (Peter Weller), who is trying to travel back in time to save his girlfriend, that it is a big mistake. While trying to talk him out of it, Bishop reveals that it has cost him his sanity trying to cope with the time travel mistake he made (when taking his son Peter, from Universe B ("over there")), back to Universe Prime. He says he "asked god for proof of forgiveness - a white tulip".
So after Peck disappears from this time line (and now Dr. Bishop has never met Peck), Bishop receives a white tulip in the mail, sent from Peck's friend at the University after she followed instructions to send that letter on that specific date. Dr. Bishop sees the white tulip as a message from god that he is forgiven.
At this point, I assume Dr Bishop never mentions this to Peter, but maybe I missed it.
The very last scene of the last episode, Peter receives the White Tulip, but this time it is addressed from Walter (not Peck) to Peter.
If Peter never saw the White Tulip, or was never told the story by Walter, then he can't understand the significance?
The very very very last scene, Peter looks up and into the camera, with a stunned look on his face - as if he knows. Does he?
(GAWD I LOVE FRINGE!)
By the way, did anyone notice this?
A final message to the fans maybe? (I'd like to think so)