You had this situation too? You open a box or other container/tool and “puff”… Some of your items are gone. I read that this happened in early access, but I didn’t know this is also present in released game and not repaired since… a year.
I think only secure items are those that you carry (of this I am not so sure now) or wear. (they don’t disappear).
Disappearing items bug should be resolved quickly - otherwise, people will drop this game (I don’t know any person who like grinding for vain; if there is no effect of grinding, meaning: disappearing items).
edit: oh, yeah… now medium tasset from armorer’s bench is gone.