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My first and only account for Skyrim and I have had Farkas traveling with me from near the beginning. I have never completed his questline. Anyway, I'm in Morvunskar searching for my drinking buddy and battling a ton of mages. All of a sudden I notice my sword wielding friend is using a staff. How did this happen? I can't equip him with anything. Is it possible he was disarmed and picked up a staff instead?

When he changes into a werewolf for the first time (in Dustman) he drops his Skyforge sword and uses an iron greatsword afterwards. Perhaps he transformed again and then lost the iron weapon as well?