During the days leading up to the discovery police have hauled in earthmoving equipment and excavators.
The discovery of the remains is the latest twist in the captivating 20-month case after the pair vanished from their Wonnagatta campsite on March 20 last year.
Police allege that Lynn murdered the duo – aged in their 70s – when he next appears in court on May 31 next year.
Hill left his Drouin home on March 19, collecting Clay from her home in Pakenham in his white Toyota LandCruiser.
They travelled via Licola, spending one night at Howitt High Plains before heading into Wonnangatta Valley.
Hill, who did not tell his wife he was with Clay, was last heard from the next day via HF radio, stating he was at Wonnangatta Valley in the Victorian Alps.
Police say other campers found Hill's vehicle the next day with signs of minor fire damage at their campsite, which was completely burned out, near the Dry River Creek Track.
Since that time, police have conducted extensive searches of the area, including by missing persons squad detectives, local police, the search and rescue squad, air wing, dog squad and even the Australian Federal Police.
Lynn was stood down from his job as a Jetstar pilot after his arrest on November 22 when heavily armed officers swarmed a remote campsite in Arbuckle Junction, 1.5 hours south of Wonnangatta.
Lynn remains in police custody and will appear for a committal mention hearing next May, charged with two counts of murder.