If a weapon is swapped between soldiers, or placed in storage, and the ammo is not full, then all ammo in the weapon is lost.
Example: Swapping the Hephaestus II with 21 ammo of 22 will lose all 21, forcing a new ammo build that costs resources.
Are you sure? Way back I saw this actually swaped ammo in inventory. If you double check there, it should be all correct. Meaning it created new ammo in your global inventory with the difference. I’m not looked at this since that time, but I’m remember that I got first impression this is something off here, but then double checked everything and it was okay but was done in a weird way where it created new full magazine and swap some for not full ammo. So if you have 5 ammo stack it doesn’t mean you have 5 full ammo. One can be half of ammo for example or whatever you got, but it doesn’t show this until you select last ammo from inventory. And if your last ammo from stack isn’t full and you do some change you can get impression it was lost. But it wasn’t, it actually was merged → two not full stack into one stack. Remember that you can’t check that because if you see for example that you have 5 stacks of ammo you can’t check how many rounds are in last stack.
So to sum up when 2 not full stuck are merged there is now one stack. You didn’t lose any single ammo in a stack, it just got merged into one stack from two not full ammo stacks. You can’t undo this action because there is no divide ammo mechanics. But it’s merged automatically if you swap ammo between soldiers.
If you will see sth else please report.
Okay I tested sth. I had one spare ammo stack in global inventory. I went with full ammo and fired one shot with this weapon type. Still got a full weapon and full ammo stack in inventory after completing the mission. I think this is calculating correctly only not showing that actually the stack in my global invetory got depleted by one shot. Otherwise it would destroyed the inventory stack when loading the spare one. This is clearly an UI bug and not displaying calculation correctly rather than destroying ammo when loading.
So when 2 stacks are merged, one stack dissapear. But you have correct number of ammo in a stack. It’s just that the UI sometimes shows ammo capacity x/x in global inventory, with x being max. But it’s not always max even it shows that way sometimes. It actually got changed. This updates when you merged ammos. That doesn’t mean that calculations are wrong. It can be only UI bug. I didn’t test enough to say when this happens but from my example UI ammo stayed full even though I’ve taken one shot. I expect when I shot enough it will disapper. Otherwise I wouldn’t need ammo and I still need to buy one.
I have checked in my play through. At first I thought, as you have described, that the ammo was in the global inventory. However on at least three occasions I have swapped between missions a weapon to a different soldier and the ammo has been lost. I know that it is lost as there where no other magazines for the ammo to be placed and the magazine simply disappeared leaving only the empty weapon.
The clearest way for anyone to check is on the occasion when you have picked up a weapon you can not manufacture. Initially it will be in the global inventory with the matching magazine. When you equip a soldier and they then use that weapon it will have a depleted magazine. Now try to swap the weapon to another soldier. For me the ammo disappears.
It is not lost. It is remembered in the game memory and saved.
But you can’t get that “not full magazine” into weapon. So when swapping weapon between soldiers you need to take care to have at least one full magazine.
Right now that 21 ammo is somewhere in the inventory but invisible. If you will go to mission and you will fire that weapon for example 10 times and go back to base its ammo will be replenished at no cost. Then you will have invisible 11 ammo left there, and full weapon again.
Previously these partly empty magazines were shown, but those were confusing the players, as they didn’t pay enough attention to the ammo indicator. They did not checked(!) if they load weapon with half-empty magazine, and they were complaining on the forum that it is possible to load weapon with such not full magazine and go like that to the mission. Even if there were flashy icons indicating that soldier’s weapon is not fully loaded(!). Thus Snapshot decided to hide these partly empty magazines and not allow them to be taken on the mission.
It’s still confusing but other way around. Like it shows ammo info but it’s not correct. If it’s not 48/48 ammo but 32/48 why show 48/48 and confuse people. They’d be better not showing any numbers in that situation.
If you have 32/48 you should not see that magazine in base inventory or even soldier’s inventory. 
Such situation is only possible when you left such number of bullets in a weapon and you haven’t replenished weapon after mission. If you will put that weapon into base inventory that magazine should dissapear (if you haven’t had 16+ ammo hidden there).
I’ve just done this test. Had one spare magazine. Went to a mission with full ammo. Shot a guy in the face. And still had full ammo in a weapon and one full spare magazine after the mission. So how this is impossible when I’ve just done this. Like it showed 48/48 before the mission and after the mission, even though the shot was taken. I understand UI didn’t show the change but the magazine didn’t dissapear and it still showed with full 48/48.
And as a whole disappering magazines and hidden ammo count that you don’t know about is terrible idea. How is this less confusing I don’t know.
Thanks for explaning Yokes.
Is it possible to have the last magazine with whatever ammo is left then available to the player?
The reason for this is so when you are using a weapon you can not yet manufacture, that hidden ammo is available as a partial magazine. I would rather have the 21 shots available now then wait till I can manufacture a magazine (if ever) sometime in the future.
I think that may be a different bug as it has also happened to me. I believe I’ve seen it reported elsewhere.
Probably you had more than 48 ammo in base store, but it showed 48/48. 
Try with completely new weapon and ammo which you haven’t found previously and it is freshly manufactured.
Yeah I know this is UI thing. I just tried to answer the OP question, that UI is not showing correct information. I just not like when it shows ammo count and you at the same time have different hidden count. This is terrible and more confusing. You don’t know real one and some hidden magazines are suddenly appering and sometimes some are disappering without you knowing when and why. This is beyond confusion. And it was done to make it less confusing.
You can ask devs to show partial magazines in base store. Probably better to use Canny than here. Maybe propose this as an option in the settings?
I agree. 
It is not my design. If they will bring back showing these partial magazines then you will need to deal with people complaining that they can bring half-empty magazine to the mission. 
Look it’s not about that. It’s about how they did this change. If you not showing partial magazines why show information about partial ammo that is not even correct. Delete this x/x as a whole and put info that individual shots are counted. How? This doesn’t really matter. It’s about not showing info that is suggesting something not true. You now have hidden ammo. What next? Hidden armor? Hidden weapons? Hidden soldiers? You can’t have hidden stuff and numbers at the same time that show something different because you have this kind of confusion and people thinking it’s not even counting it properly and stuff is disappearing when it’s not.
As I said. I agree…
part about people complaining was just about outcome of restoring feature to its previous state. If Snapshot can make it better then I would be glad. If they would want even to try to change that instead of fixing other stuff.
I just tested today and found that partial magazines for something you CANT manufacture get lost
They shouldn’t get lost, single bullets of a partial magazine are saved in the background of the global store and are not shown in the UI, even for something you can’t manufacture. At least this was the case the last time I tested it.
This used to happen with bandit weapons. I thought they fixed it, but maybe i just dont see it now because we can manufacture bandit weapons now. It could be that a partial magazine only gets lost when there is no stack in stores to add it to. I un-equipped a hel-2 with 5/6 ammo, there were no spare mags in stores, then re-equipped, and now no ammo at all. I’ll test it today with whatever other gear i have and file a bug report
Partial ammunition (i.e. no full magazines) will not be used to load weapons in the equipment screen but they are not lost at all. IIRC this loading of partial magazines when equipping soldiers was changed in the past because people complained about half filled weapons when equipping soldiers.
It is hard to test if these single bullets are really lost. The way I did was to unload a weapon with a partial filled magazine and without any magazine in the store (I gave them them to other soldiers). Then this partial ammunition is no longer visible, still no magazine in the store. Then re-equip the weapon which now is total empty and give one magazine from the other soldier to the one with the empty weapon. Then I started a mission, reloaded in mission so the weapon is full, shoot once, exit mission and then his weapon was automatically reloaded with the partial ammunition that still is in the global store even when it is not shown.
It is been a while since I’ve tested it this way, but I think it was not changed, not sure tho.