All these answers miss the point that when Hackworth is being sentenced by Judge fang he subverts the books to be linked to the missing primer (the one owned by Nell).
"At this point, John Percival Hackworth, almost without thinking about
it and without appreciating the ramifications of what he was doing,
devised a trick and slipped it in under the radar of the Judge and Dr.
X and all of the other people in the theatre, who were better at
noticing tricks than most other people in the world. “While I’m at it,
if it pleases the court, I can also,” Hackworth said, most
obsequiously, “make changes in the content so that it will be more
suitable for the unique cultural requirements of the Han readership.
But it will take some time.” "
He basically takes a subversive book makes it more Chinese and respectful of authority but he makes the authority the owner of the missing book.(Even Hackworth has no idea who owns this book at this stage.) Thus the hunt for Princess Nell by the mouse army.
"Hackworth sat down across the table from Dr. X. A young woman padded
out of the kitchen on silk slippers and gave Hackworth his own tumbler
full of green tea. Watching her mince away, Hackworth was only mildly
shocked to see that her feet were no more than four inches long. There
must be better ways to do it now, maybe by regulating the growth of
the tarsal bones during adolescence. It probably didn’t even hurt.
Realizing this, Hackworth also realized, for the first time, that he
had done the right thing ten years ago."
So the girls will become Leaders of a new way, with out the foot deforming etc, but with the use of the seed.
"The provisional commanders of her divisions stood foremost, as did
her provisional ministers of defense, of state, and of research and
development, all of them bowing to Nell, not with a Chinese bow or a
Victorian one but something they’d come up with that was in between."
The book of the seed is inside Nell's Primer at the end and being worked on by the drummers even as they remove Miranda from the Drummer community.
"“Hackworth is the Alchemist,” Nell said, “and he is using the wet Net
to design the Seed.”"
As for them both leaving the Middle Kingdom they attack the fist checkpoints while Hackworth is watching and tie them up. This is after they discover their leader in the Primer after Nell breaks the last turing machine and the land beyond disappears. So they meet Nell in the book get turned into humans in their primers and then in real life head to where Nell is as an army of followers.