The Return of the Nephilim
I think the answer about how the nephilim could have returned despite the flood is simple. The mistake that people make is assuming that God sent the flood to destroy the earth "primarily because" of the existence of the nephilim. They assume that because the passage mentions that Moses was "perfect in his generations." But I think people are reading way too much into that.
Nowhere does scripture say that God sent the flood because of the nephilim. What the scripture DOES say is that God was grieved in His heart because mankind was thinking and doing evil "continually." The passage also says that "there were giants in those days, AND AFTERWARD..."
Thus, there is a crystal clear expectation (before the flood even occurs) that the nephilim will exist AFTER the flood. God never would have let that happen if His purpose for the flood was to destroy the nephilim in the first place.
So the nephilim reappeared because, even after the flood, some demons still interbred with women: "there were giants in those days, AND AFTERWARD, when the sons of men came into the daughters of men..."
The verse explains very clearly how the nephilim come into being. It is through the interbreeding of demons with women.
Since Noah was "perfect in his generations"
he didn't have any of this demonic DNA and could not have passed it to any of his descendents. The nephilim HAD to reappear because of more interbreeding AFTER the flood.