To anyone noticing issues with Fallen Empires panicking about Cetana when you select any option in the Crisis Sequence menu - I am aware of this issue and I have highlighted why it's happening and what this mod can do to resolve it in the Oddities, Errors, Additions discussion.

This is a Vanilla bug, if Cetana dies and a Cosmogenesis FE is created then it will panic about Cetana. There is no check to see if she's dead.