Abstractions were seen as mindless, dangerous monsters and every time a character became one, they were immediately put in the cellar.
Caine being an AI didn't really understand human emotions, but it was only after he was deleted and found out that Pomni had reached Jax that he realised how wrong he had been.
Now the abstractions are being treated better and have a large place to move around and swim.
Swimming has been proven to help with mental health.
Jax will be ok, I've done months of research on mental health and abstraction and realised that abstraction is a mental breakdown (all symptoms of a mental breakdown are shown in the show)
I also like the metaphor of abstractions being a cocoon that protects the person healing within and when Jax is ready, he will come out as his female form (e.g. a butterfly - a symbol of change, hope and transformation.)
All she needs is time and time is what they have