I'm up to the section where you restart the generator. In one room I picked up a battery. Then I got killed. When the checkpoint loads I'm back to my previous number of batteries but it's no longer in the room either.

The savegame is not a proper save, just a checkpoint. So if you die, you still get to keep all items that you picked up before death, including documents. One added "bonus" of dying is that you restart with a fully charged battery.