Seems he encountered something overpowering. Hostile tribe? Disease? Giant snake? Something more menacing? Source: What the Hell Happened to the Man Who Mapped the Amazon? - adventure journal
In the movie The Lost City of Z, it is implied that he and his son were captured and killed by hostile natives. The area in which they disappeared was known to have some very unsavory tribes, some of which practiced canibalism. The Lost City of Z (film) - Wikipedia