I've solved this problem!
There are a set of 4 notes and a set of 4 research notes, but only the "notes" are important. Disregard the research notes.
After you kill everyone (or spare Uariki...that part doesn't matter), and take the notes off their bodies, only 3 notes show in the quest tab of your inventory. Pelden's note is missing. You will see it on his body, but it won't transfer to your inventory.
So after you kill Pelden, read his note (right click on it) BEFORE adding it to your inventory. It will then disappear, but that doesn't matter!