Well, all of who? He didn't actually say all of mankind. And I'd argue that maybe the flood did happen, and there was a guy named Noah who built an ark and survived it. But that it didn't kill everyone but 8 people, that is, it wasn't global. The relevance of the story was, not that the Flood was global, but that it swept away those who weren't paying attention to Noah's ark-building and whatever he might've said to them about it.
Either way, it's more complicated than just that one example. I'm sure Jesus existed, just as I'm sure Noah existed; but I think every detail may not necessarily be exactly as it really happened, since nobody could actually record every detail--and even Noah's story isn't written down until well into (or after) the time of Moses. I don't think the Flood reference discredits Jesus. It's an example he would likely use as his audience was familiar with it.