Even though i can't currently play the game. I found inventory maintenance very important with companions but most important was leaving them out of unnecessary situations (confined spaces, dangerous combat, unnecessary accompaniment on fast travel errands. I typically parked them in the Novak hotel room safe house or at least the inner gate of a vault when I didn't want to worry about keeping tabs on their companionship. It's not a fix, but it helped with always losing them and potentially losing items when quest chains required they leVe company.