A lot of the melee weapons that were never updated are gradually being removed from the game, I just haven't hunted them all down yet.
A lot of the stuff being discussed here is in my documentation, though it is very long and I suppose I can't blame most for not taking an hour to wade through it. The game engine doesn't deal well with containment. If an item (like a fusion battery) is meant to be removed on exit from a mission, and the person holding that item is inside a vehicle, the item won't disappear. This cannot be fixed. You used to then see "No description available" for all these items, which I did fix in Redux.
EDITED:
I see what's happening in the Preoria mission. It's a rather obscure bug, good job on finding it. This problem only happens if you reload a saved game that was saved on the Preoria map. Since the battery is flagged non-lootable, when you reload your savegame the item disappears from the Elder's inventory and therefore he can't give it to you even though he says he does, and when you then go to the exit grid since the item isn't in your characters' inventory you don't get credit for it. This problem does not occur if you play the mission straight through without reloading.
The same thing used to happen with the Librarian in Macomb, but the way I fixed that problem won't be of use here so we are left with two ways to resolve this Fusion battery issue. Which one would players find most helpful?
A) When you talk to the Elder, if no villagers were killed, a variable is set. Therefore you will get credit in your debriefing for obtaining four batteries, even though the fourth will not be shown in your inventory if you reloaded a saved game on that map.
B) I could make an invisible entity standing next to the Elder who hands the battery to the nearest player-character when talking to the Elder. The trouble with this approach is, if combat has occurred and the Elder has run across the map, then the invisible entity will be too far away to hand over the battery. In other words, this solution isn't foolproof, even though it is the only way to actually place the battery in your inventory if you've reloaded a saved game.
Comments are welcomed on this issue. There will be a minor update in a few weeks to address whatever we decide on this, as well as a few very minor things I forgot to include in 1.2, so keep those bug reports coming.