Here's one possible chain of events regarding how the inverting eyepiece became associated with AE.
-- Nov-Dec 1939: Sextant box found by or given to native worker by USS Bushnell crewmember.
-- Nov-Dec 1939: Native worker discovers eyepiece in sextant box and having no use for it, throws it away, probably shortly after box comes into his possession.
-- April 1940: Sextant box is now being used as storage or carrying case by work party member(s) who found the skull. Box mistakenly left at 7-Site by work party after burying the skull.
-- September 1940: Box found by GBG at 7-Site and mistakenly associated with Earhart
-- September 1940: GBG returns to village with box and other artifacts. GBG is told by someone that a piece GBG believes to be an inverting eyepiece, based on description he is given, had been found and thrown away, but doesn't hear, miss-understands or isn't told the when or where. GBG assumes teller means that a member of party who first found/buried skull also found object (eyepiece) in sextant box and tossed it away. GBG subsequently never asks or learns that box was carried to the site by the work party. He had no reason to ask as he had already associated the box with the skeleton in his own mind.
I'm sure they might be other ways as well.