I'd encountered this issue myself earlier today, and the problem was indeed Stoffe's Handmaiden Appearance 1.1 mod -- I fixed it by manually removing all of the files in my override created by the tslpatcher (referring to the backup folder) except the appearance.2da file. (So all .utc, .uti, .ncs, .nss files were pulled out of the override folder) I reloaded a save right after the Dantooine council conclusion, but before leaving the rebuilt enclave and triggering the load to the Telos academy. The fight worked as intended (including the stun/kill mechanic) and I was able to progress. (For what it might be worth, I was also running the Extended Enclave mod and installed it after the Handmaiden Appearance pack)