Masih

I too had this same issue, but it was after stunning the other Handmaidens. What brought me out of the fight with the Handmaidens, and started the fight with Atris was running around the Academy hysterically trying to figure out what to do then succumbing to my base anger and attacking a handmaiden that was already stunned. Once I unleashed my horror, they went back to being stunned and Atris walked out. Cue fight with her, Exile shows up, etc.

I ended up reloading. I didn't see an option for it if you mean under the hk50 schematics choice.

So I go to the end of the factory, uploaded behavior core to the hk51 and restarted its production. It is now on the secondary line. However, I am unable to set it to the primary line due to being unable to shut down the hk50 line (I accidentally downloaded the hk50 behavior core). Someone suggested going back to the droid who wipes your memory earlier on in the factory, yet I am unable to leave the factory sublevel. Is there a way to remove the hk50 core, like the text suggests, or am I now forever stuck?