Loading into new scenes (i.e. going back to homebase/loading in a new region) in coop makes it so items disappear for the person who isn't the host. The host can make the items reappear by grabbing them off of the friend/the friend rejoins and the items load as normal. This doesn't happen all the time, but enough for it to be a minor annoyance when it does happen.
I'm using a Quest 3 via SteamVR link.