There's actually a very easy way to re-equip your soldiers in Apocalypse: you can (I think shift-click) select multiple soldiers to change their equipment all at once. I would re-equip my soldiers based on categories: some with machineguns and some with autocannons, and they all had the same grenade setup. I'd just select all the autocannon soldiers and fix them, then select all the machinegun soldiers and fix them. You only see specifically what the orange-boxed soldier has, so you won't see right away if some of the yellow-boxed soldiers are missing grenades or ammo, but if you pick up each clip and grenade and place it right back in its spot, it will re-fill all selected soldiers. I think the weapons re-load themselves, but you can easily re-load them manually as well.
It's a lot more difficult if you have several different layouts spread across your soldiers.
