Also this. Where does the Water fall go in Enies Lobby? If there was a sea floor, it would've risen back up, but it doesn't.
My theory is that, the weapon that does this, is actually a massive teleporter.
But not a normal teleporter. A permanent teleporter that displaces whatever it targets.
So basically, Lulusia, and Ennies Lobby's missing piece, got displaced to elsewhere.
And the holes made from that are actually kinda like worm holes. So the water falling in is also getting teleported. That's why it never fills up.