This is really frustrating in the moment, but there's actually a reason why this happens. If you've finished Flynn's route you've probably figured it out yourself by now
This is something of a midquel, taking place during the several-month tour you and Amicus that's skipped over during Adastra. Khemia is a sequel that takes place during the interim after Adastra but before you and Amicus reunite; you play as a completely different character in Khemia.
