This issue has persisted throughout the Arma 2 campeign but it has not become an issue for me until the Badlands mission.
The issue is basically this - I am unable to buy weapons or rearm my current weapons without my existing weapons completely disappearing from my gear. Note that I am saying that this happens when I rearm/buy, not upgrade. For example in the Badlands mission I am currently setting up my base and in need of an RPG. I go to my barracks and choose 'buy weapons' immediately upon entering the screen my current gear vanishes except for my M4 magazines, everything from my M9 to my GL rounds vanish. If I click cancel/close without buying or rearming I am left empty handed. The same happens when I merely choose rearm or if I attempt to buy an RPG (which I need). Again, note that this is when buying weapons that are not replacing my current loadout (like buying an RPG to fill my empty launcher slot, or buying ammo mags for my M4). Everything vanishes and there is no way I am able to get them back.