Their new handler Satsuki made a point not to say Eliza was a hero unlike Autumn and Chrys. It's true that she was defeated, but she also helped before that boss fight. The side ship teasing(?) continues with Chrys and the kid.
I probably shouldn't be trying to think about this too much, so far it's mostly an excuse to draw girls in questionable mid-air poses when it's not about ero-guro.