First of all I must state that this happens on persistence enabled servers.
I know about 3 cases (me included) of weapons dissapearing.

The second primary weapon (the one in your hands, not ht one on your back) dissapears as I deducted after a while (let's say 30 minutes in game).
In my case, the server restarted, after I joined, I was missing my M4. All other stuff laying on the ground before the restart was spawned back (except a pistol in one backpack that was spawned with a delay). I tried to relog to no avail.

Another friend of mine reported that he also had a weapon dissapearing from his hands on a private persistence enabled server. Moments before he put it down to eat.

The third dissapearance happened to another buddy of mine while aiming with the weapon.