Although the Convoy members were to some degree insulated from diseases endured by much of the Chinese population by adequate food and shelter and the best available medical services on hand, they were not immune to these or other dangers. After some counterproductive attempts to share with others more needy than themselves they quickly learnt to maintain their own rations if they were to function. Anthony Perry recalled how on landing in Kunming his first instruction was in sterilisation of cooking utensils and in not using the face cloths provided at the Fan Diens for fear of contracting trachoma.

Evacuated from Burma to Calcutta and weak from dysentery, Bill Brough was diagnosed with malignant sub-tertian malaria which became cerebral malaria. After slipping into a 5 day coma, receiving the last rites and having had his temperature reach 107.8^o he recovered, but was left partiallydeaf for the rest of his life by the medication he had received. At the same time in China, in June 1942, Doug Hardy, weakened by dysentery, died of typhus, as did John Briggs.

After administering some 10,000 typhus vaccinations – but not his own - Dr Donald Hankey of the British Red Cross but attached to the Unit, also died and Dr Quentin Boyd who had been too assiduous in his anti malarial dosage, died of atabrin poisoning. Remarkably, no members perished on the mountain roads but Dr Clement White was fatally injured in a fall from a stationwagon and Brian Sorensen was lost in an aeroplane crash just after he had left the Unit.

Pip Rivett and Peter Mason both contracted polio shortly after arrival in China; Peter survived but Pip did not. Canadian schoolteacher Robert Waldie succumbed to complications after appendicitis. Sydney Bailey returned home carrying the bilharzia parasite which left him in pain for the rest of his life, and many others endured periodic bouts of dysentery and malaria which incapacitated them for weeks.

The FAU had other losses elsewhere including its overall leader Tom Tanner and Head of Personnel Peter Hume whose ship was lost on their way to China for an inspection.

Tom Thompson got away with his life when attacked by bandits with swords after his truck broke down. His ulna nerve was severed and his arm and hopes of resuming his career as a PE instructor were shattered. Despite undergoing three unsuccessful operations to restore his arm conducted by Bob McClure, he was not deterred from travelling for three days to plead against the execution of the bandits at their trial.