Hello,
I seem to have an issue where Benweth went missing, but I didn't kill him.
Without progressing far into the quest, I went up to the command space, sneaked and triggered the bell to open the secret door. When I stepped it, the game triggered a conversation with the captain, which was supposed to end in combat, but since I was sneaking, the combat didn't trigger. He was over my level by two skulls, so I simply walked away, without engaging in combat, and certainly not killing him.