Seeing the similar issues here
https://community.amplitude-studios.com/amplitude-studios/endless-dungeon/bugs/331-fassie-s-first-chips-slot-is-locked-after-completed-the-quest?page=1
Did this happened to you in a single run from start to finish or did you guys also stop the session and continue?
Completed Sweeper's second quest in Co-Op with a friend who was the host, and even got the game's in-run notification of quest completion as well as lore unlock. However, Sweeper is still restricted to one chip slot. Friend as host had similar issues with Bunker and Zed.