When the Bible says that the entire world was flooded, that might not necessarily mean that the entire surface of the planet was under water. When Alexander the Great completed his conquests, he said that he was disappointed because there were no more lands to conquer. The thing is, there was still Southern Africa, Northern Europe, Eastern and Northern Asia. That's not even mentioning the Pacific Islands, Antartica, and the Americas, which he didn't know existed. At that time in history, the Middle East and the Mediterranean area was the entire known world. Based on the geography, it is not unlikely that that part of the world could have been flooded at some point in the past few dozen eons.