In one cut scene Drake removes his necklace however, later on when talking to Roman across two opposite glass booths, (end of Chapter 19) the necklace reappears in part of the cut scene.
During the El Goddamn Dorado scene, the hat wearing mercenary next to Drake switches places with the other mercenary and back again during Roman's coughing.
Nate realizes that El Dorado refers to the statue, not a city, when pointing out that "El Dorado" means "the golden man". It means "the gilded one", and the real El Dorado was a tribal chief who covered himself in gold dust.