Well, now in the place where her hut used to be there's a lot of empty collapsed tunnels that make kind of an ugly hole in her Clay network, but on the plus side, she wasn't just murdered by a Sentinel. Call it a win.
Also, apparently the lowest layer of the network is deep enough underground that Sentinels can't see her down there. She adjusts her tunneling strategy accordingly, and sends a few Tunnelers north to see if they can cross the border safely as long as they do it from far enough down.
Her original body arrives in a Tunneler-carved cave, not far from the bottom of Lake Champlain. No one's going to hear her scream down here; she lays her egg, hatches baby Third Naomi, and starts feeding her Clay. Meanwhile, Second Naomi keeps hatching Tunnelers to expand the network.