If that part of the gospel was actually written in the 2nd Century, I would assume that the knowledge of the pool itself was still there 200 years later - it didnt become forgotten until later.
The oral tradition was pretty strong back then - its quite possible that the Gospel of John was handed down in an oral tradition and not formally recorded until some generations had passed. Locals of the 2nd Century would probably have a very good idea of how Jerusalem was laid out in the time of Christ, but some centuries later, after the various barbarian and Islamic invasions, the Crusades and however many temporary evacuations and resettlements of Jerusalem, local knowledge probably lost a lot of old geographic reference points.
Seriously, how many people today are aware of pools that existed in 1805? There just weren't that many written records back then, expecially after Rome's onslought.