While I don't doubt that there will be some genuinely ancient stuff now underwater, it seems unlikely that it would shift the global picture of the emergence of settle agricultural societies that much. Most "cradles of civilisation" are inland river valleys - Tigris, Euphrates, Nile, Yellow River, Yangtze, Indus, Tehuacan - with the exception being sites in Peru. Being by the coast only becomes useful once you get good at building ships, after all

I'm not in any way actually qualified on this though, so if there's some actual research saying otherwise I'd be delighted to read it. There really was a lot of sea level rise in the ~10,000 years before we know that agriculture got going, so it would make a lot of sense that at least some stuff got flooded