Flora was born at Milton on South Uist where her father was a tenant farmer. She completed her schooling in Edinburgh and was visiting her brother in South Uist in 1746 when she was asked to assist Bonnie Prince Charlie, on the run after the defeat of the Jacobite Uprising at the Battle of Culloden. He was to be disguised in a frock as "Betty Burke" an Irish maidservant. She thought the scheme "fantastical" but was persuaded to go ahead, perhaps by the Prince. They sailed from Benbecula on 27 June 1746 to Skye. They hid overnight in a cottage and then travelled, over the next few days, overland to Portree, at one point avoiding some redcoat government troops. When he left to travel to the island of Raasay and a ship to take him back to France, the Prince gave Flora a locket with his portrait, saying "I hope, madam, that we may meet in St James's yet" but she never saw him again.
Flora was arrested and imprisoned in Dunstaffnage Castle and then spent some time in the Tower of London but was released in 1747 under a general amnesty. She married Allan Macdonald of Kingsburgh, a kinsman, in 1750.
Block House She then emigrated to North Carolina with her husband. While initially successful farmers, Flora's husband joined a regiment of Royal Highland Emigrants supporting the Hanoverians at the start of the American War of Independence. He was captured at the battle of Moore's Creek and, after a spell in captivity, was expelled to Nova Scotia. They lived for a time in 1779 in a block house there - it is now the last remaining building of this type in the province (see illustration). She then returned to Skye with her husband.
She later met Samuel Johnson, the English essayist during his tour of Scotland with James Boswell. Johnson described her as "a woman of middle stature, soft features, elegant manners and gentle presence." He also said of her: "Her name will be mentioned in history, and if courage and fidelity be virtues, mentioned with honour."