At the Restoration of Charles II, Gernon, like most of the Irish judges who had acknowledged the authority of Cromwell, was pardoned for his disloyalty, and his pension from Cromwell of 100 marks a year was continued by the new Government. He was not restored to his old office of second justice in Munster, which was given to John Nayler, but this is hardly surprising since he was now at least 80 years old. The office of Lord President of Munster, and the provincial Court, were abolished in 1672: Gernon may still have been alive then, although he was dead in 1673 when probate of his estate was granted to Thomas Sheridan. In his later years he lived mainly in Cork. Although Archbishop Ussher praised Mrs Gernon highly , calling her "a lady of quality", little else seems to be known of her, apart from the fact that she had a family connection with Henry Pierrepont, 1st Marquess of Dorchester, which was useful to her husband. From Luke's petition to Cromwell for redress we know that they had four children, of whom one died young as a result of the family's sufferings in the Rebellion. A surviving daughter, Martha, married Major Nicholas Brady and was the mother of Nicholas Brady (1659–1726), co-author with Nahum Tate of "New Version of the Psalms of David (1"696), a metrical version of the Psalms. A later distinguished descendant of Gernon was Maziere Brady (1796–1871), Lord Chancellor of Ireland. The manuscript called "A Discourse of Ireland", first published in 1904, seems to have been a long letter which Gernon wrote to an unnamed friend in England. The tone of the "Discourse" is generally friendly to the Irish people but it is also somewhat condescending, and written entirely from the viewpoint of an English colonist. Gernon, unlike many Englishmen of his era, did not regard the Irish people as being either savage or uncivilised, but believes that they will benefit from English influences; rather coarsely, Ireland is described as a young woman or "nymph" who needs to be "occupied". Significantly he heaps praise on Richard Boyle, 1st Earl of Cork, for many years the dominant English settler in Munster, (and whose son Lord Orrery was his friend and patron), especially for his improvements to the recently founded town of Bandon (although Lord Cork was not, as he sometimes claimed, the actual founder of Bandon).