By October 1763 his health had deteriorated to the point that he was unable to write letters we are told by Robertson of Strowan who was also an exile in France and had been corresponding with Cluny over the years. Apparently the letter that led him to that conclusion had been written by Lady Cluny or daughter Margaret. Based on Strowan's reply, that letter also appears to have contained a request from Cluny for advice on the best way to ship goods from Badenoch to Dunkirk -- the Prince's silver plate now seems to be of pressing concern to the stricken man.
During the last ten days of January 1764, Cluny was attended by the Rev. John Maitland, a Scottish Episcopal minister who had served the Jacobite cause and been exiled as a result. In attending to Cluny's spiritual needs Maitland tells us that Cluny, "in the most solemn manner that a dying person . . . could, declared that he never saw the [Prince's jewels] or knew anything about them: that the plate was safe, and that he had some time ago transmitted orders for the delivery of it." He asked Maitland to inform the Prince of this thus fulfilling the promise he had made to him in June 1757.
During those ten days Cluny also was able to instruct various merchants as to the disposal of his effects to pay some of his debts and to request that they arrange for Lady Cluny, Margaret and Mrs. Nicholson to travel to London after his death. That came on 30th January 1764 in the presence of his wife and daughter, Mrs. Nicholson, his friend, Captain Lachlan Mackintosh and the Rev. Maitland. The circumstances of his death were recorded in a letter written on 31st January by the merchant, David Gregorie which tells us that he was to be buried that evening in "a private manner in the Garden of the Carmelites, which the Lady prefers to a Publick burial attended with the honours of War." A second letter written by Captain Mackintosh and addressed to Cluny's brother, Major John Macpherson provides a rich and moving portrait of Cluny's last days. The location of his grave has been lost.
No sooner had these letters been sent than Cluny's old comrades, Breakachy and Benchar, arrived on a repeat visit from the year before, probably aware that he was dying. They were too late for Cluny's last moments but they were present for his interment. Their arrival and subsequent events were reported to the Prince by the Rev. Maitland in February who informed him that both of the newcomers swore that they knew of no jewellery; that the plate was safe in the custody of Cluny's brother, Lachlan and that they had seen Cluny's order for it to be sent to the Prince. However, they stated that the custodian would not send the plate unless he had a signed release from the Prince.
Lady Cluny's sad journey back to Scotland began on 16th February leaving behind a tangled state of financial affairs that are too complicated to discuss here. Her health was a matter of concern and she was not informed that her half- brother, Archibald Campbell Frazer of London, with whom she was to stay with there had become bankrupt. According to a letter by Benchar to Lady Cluny's full brother, Archibald Fraser of Lovat, the funds for her stay in London and subsequent journey to Edinburgh were substantially aided by a Mr. John McIntosh who he wrote "Shou'd be gratefully Acknowledged by every person concerned in the Lady or her Misfortunated family." In any event, Lady Cluny and her party stayed in London until 9th March when she left by stagecoach for Edinburgh. There too, Benchar tells us that, she was well taken care of and told not to be concerned with finances. She stayed there until May when travel to the Highlands was easier and took possession of Cluny Mains from her brother-in-law, Captain Lachlan on Whitsun term day, 15th May 1764.