The story, in my opinion, has a narrative outline that is lost when mulling over details like this. If you think of it like a play it makes much more sense.
Characters:
YHWH Creator of the Universe
Noah and his Family
The Bad Humans
The Bad Spirits
The Nephilim
Plot:
YHWH created everything and was displeased with the way his creation was going about their business. He decided action was necessary. This choice was because of an intermingling of creations from the realm which he resided and the realm of the humans. This intermingling created a hybrid race between the worlds. This new race was not human, but was not spirit either and decided to enslave the humans and ignore the rules of the spirit realm. This went on without intervention because of the rules of the spirit realm which were now being broken in brazen manner. The Nephilim were not subject to the old rules being from both flesh and spirit. Only at this point does YHWH decide to intervene when one side is able to cheat so-to-speak.
YHWH decides to take the problem at it's core. The very ability of the spirit realm and the flesh realm to intermingle to the point of reproduction. His solution in his devine wisdom was to annihilate all life on the earth essentially severing the connection with a reboot. This was the only way to truly restart without the open connection to the spirit realm. This time around that hole would be filled and the Nephilim will be kept from coming into existence. This will require a long term strategy that differs from anything previous.
^ I don't even have to mention the means of which the annilation of all life on earth takes place. That is a detail that can be left out, or even changed, without losing true to the original message of the story. Which is that God provides a life boat when life is capsizing even if it's our own fault. It is a story about who he picks for his reboots. According to one of these doomsday stories, the Great Flood Story of the Bible, the criteria is contingent on righteousness. Noah was blameless and upright. So that's how to beat the system: love.
-Sab