Due to her interaction with Cassie, Aftran decided to let her host, Karen, go free. Near the end of #19 The Departure, Aftran is inside Karen's head, in the woods, talking to Jake. Karen's body is very badly injured.
At the very end of the book, Cassie meets Karen, finding that she is indeed free.
In #29, Aftran is found to also actually be unhosted in the pool, as promised. She also risks her life to save Ax's, then voluntarily leaves Ax's head.
Aftran freed Karen and then went back to the Yeerk pool to live there without a host.
How did Aftran get down to the pool, if not through Karen's body? How could a lone Yeerk travel down to the pool without a host? And if she used Karen's body to get down there, the Yeerks would not let Karen go, they'd either give her to another Yeerk or kill her (due to her injuries).
One thing I can think of is that Aftran could have done something like what Illim, Tidwell and Cassie did in #29. For example, Aftran could have traveled to Tidwell's house in Karen's body. She could have then left Karen's body. Tidwell and Illim could have then taken Aftran to the Yeerk pool in a container, like he did to Cassie's Yeerk-morph in #29.
However, Aftran is thought to have been one of the first members of the Yeerk Peace Movement. And she only joined/formed the Movement after and due to her interactions with Cassie. This would indicate that the Movement might not have existed at the time. If it did, could Aftran have had connections with it? At the time of meeting Cassie in the woods, Aftran seemed like a normal, aggressive, unsympathetic Yeerk.
Assuming that she didn't have any connections to anyone in the Yeerk Peace Movement at the time, how could she make it down to the Yeerk pool without Karen?
I've also considered the possibility that when Cassie met Karen at the end of #29, Aftran was actually still in Karen, pretending to be the free Karen. But then, how did Aftran end up unhosted in the pool (as she did) without giving up Karen to another Yeerk? If another Yeerk took over Karen's body, then the Yeerks would have learned about the Animorphs from Karen's memories. That didn't happen.
How did Aftran make it down to the pool without Karen?
Assuming she somehow did, could Karen remain free? If Karen was once a controller, would the Yeerks wonder what happened to her? She was a small child, and the Yeerks were tracking her dad. When Aftran was being held in the pool, unhosted, suspected of treason, would the Yeerks perhaps have wondered what happened to Aftran's previous host? If they did recapture Karen, her mind would contain information about the Animorphs.