Nyx considered her creation's request to be absurd.
Watch over a single bloodline of humans for eternity??
Laughable!
She had neither the time, nor the patience to do… okay, so maybe she did have the time.
But she still didn't have the patience!
Nyx dismissed the idea without a second thought, but kept the soul of her experiment in her own personal custody.
It wasn't intended to be cruel, but to ensure that no one found out what she'd done, she couldn't risk letting the monster's soul rest in the Elysian Fields or any other afterlife.
Hades was a sort of stickler about his responsibilities and kingdom, so Nyx didn't know how he would react to the soul of a large monstrous snake suddenly taking a nap in his grassy pastures.
As such, she placed the soul in a small wooden box that she imbued with the power to create the ideal 'rest' of the inhabitant.