During the reign of Mary, the monks retook possession of Timoleague Abbey; and in 1603, the Catholics again took possession, and completely repaired it in every part. In 1518, Edmund Courcy, Bishop of Ross, was buried here; he built the square tower, now so conspicuous an ornament, and also the dormitory and library. It was for several centuries the burial-place of the powerful families of Mac Carty Reagh, de Courcy, O'Cullan, O'Hea and others. The castle belonging to Sir Roger Shaughnessy was besieged and burned in 1642 by Lord Forbes, who then set sail for the Shannon. It was also again taken from the Irish, in 1643, by Colonel Myn.
Following the outbreak of the October 1641 rebellion, the 5th earl of Clanricard (qv) remained loyal to the king and O'Shaughnessy did likewise. In 1642 his first wife, Ellis Lynch, having died, he married Julia Barry, widow of David Barry (qv), Viscount Barrymore. This marriage brought the Barry estate around Timoleague under his care, but Timoleague was being besieged by protestant troops and the estates were devastated. O'Shaughnessy appears to have spent much of 1642–3 in Munster trying to convince the protestant forces there of his loyalty. Even after the cessation between the catholic confederacy and the Irish royalists in September 1643, he could not gain control of the Barry estates. Meanwhile, during his absence in Munster, his son and heir Dermot joined the confederacy and began paying money to it out of his father's estates. This move may have been with the permission of Sir Roger, who now began to use his influence within the confederacy on behalf of Clanricard and the royalists. However, he declined to play any administrative role within the confederacy, leaving that to Dermot. Despite his effective membership of the confederacy, about August 1646 he became the royalist deputy governor of Connaught to Clanricard. In 1649–50 he commanded a troop of horse in the royalist army. He had died by 30 January 1650. With his first wife, Ellis, he had two children, Sir Dermot and Julia. There is a portrait of Sir Roger in Kilkenny Castle.