Roger O'Shaughnessy was not a baronet or knight, but seems to have been accorded a title by usage. His ancestor surrendered the territory of his sept to King Henry VIII and had a regrant of same. He was knighted by that monarch, and all the succeeding chiefs of the name were knights or at least so styled. This led to the erroneous belief that they were baronets, and the above Roger was described as such in Lodge's Peerage. But in his attainder and other contemporary official records he is styled Esq.16

Roger was attainted in 1688, and his estates were granted to Thomas Prendergast.16

Chancery Bill 26 Mar 1736--Thomas Prendergast v. James Butler:
Humbly complaining showeth unto your lordship, your orator, thomas Prendergast filed his original Bill on 13 Feb 1731 against Theobald, grandson and heir of Sir Theobald Butler, Councillor at law, William Moore and Mary his wife, and Hellen Butler als O'Shaughnessy, one of the daughters of Sir Roger O'Shaughnessy, who was seized of the lands of Gortervagher in the Co of Galway, and that the said Sir Roger O'Shaughnessy was attainted for high treason in 1688, and that said lands were granted by Patent dated 1697 to your Suppliant's father, Sir Thomas Prendergast . . . received from William Moore or Mary his wife, daughter of Sir Roger O'Shaughnessy or from Helen Kelly or from her daughter Hellen Butler als O'Shaughnessy.16

Theobald Butler married secondly, 1700 (marriage settlement Oct 1700) Helena O'Shaughnessy, daughter of Captain Roger O'Shaughnessy of Gort, Co Galway, chief of his name, by his wife, Hon. Helen O'Brien, daughter of Conor, 2nd Viscount Clare. Through this alliance the Butlers of Cregg became heirs-general of the O'Shaughnessies of Gort on the death without issue of Joseph O'Shaughnessy, last chief of Cineal Aodh, in 1783, and the crozier of their venerated ancestor, St. Colman MacDuagh, passed into the possession of the Butlers.16

The Jacobite War in Ireland
On March 12, 1689, King James II, having fled his kingdom following the successful invasion of England by William of Orange, landed at Kinsale with the French ambassador, Count D'Avaux, Lord Melfort, James's Scottish secretary, two of the King's illegitimate sons, and 200 Irish and French officers, including Patrick Sarsfield. The faithful Earl of Tyrconnell, who had been mustering an Irish army, was made a duke. Wasting no time, James and the army marched to Derry, a pivotal town in James' plan of securing Ireland against William.
However, Derry did not surrender to the King's Irish army, nor did Enniskillen.There was constant bickering between the Irish and French, leading to serious problems with the morale of the army. After the disastrous rout of the Jacobite troops at The Battle of the Boyne, James left Ireland and returned to France, where he remained for the rest of the war. When William finally abandoned the first siege of Limerick in September 1690, it was not because he believed he had been beaten, but because the wider war on the Continent required his urgent presence. If William had not had this second war to occupy he and his army, there can be little doubt that the war in Ireland could have been concluded much more swiftly. The proof of this is shown by the way Marlborough, less than a month after William left Ireland, succeeded in capturing Cork and Kinsale. The Williamite forces were in control of the north, east and south of the country by the beginning of 1691. St Ruth, the most competent and experienced military leader sent by Louis to aid the Irish, managed to put new life back into the Jacobites in the spring and early summer of 1691. But the loss of Athlone in July, followed by the crushing Jacobite defeat at Aughrim, which also saw the death of St Ruth and capture and death of many of the Irish gentry, saw the war enter its final act.
Galway surrendered in less than a week. Captain Arthur French, of the Tyrone family, was Mayor of Galway at the time of Galway's surrender. In addition, many members of the old Tribe families, as well as the native Irish gentry, fought for James, among them Sir Roger O'Shaughnessy and his son, Charles; Oliver Martyn of Tullira; Pierce Lynch of Rafiladown; Butler of Bunnahow and Butler of Ballygegan and Cregg; Sir Richard Blake of Ardfry, Speaker of the Supreme Council of the Confederate Catholics of Ireland; Darcy of Kiltulla; Francis Blake; various Lynches; various Kirwans, including John Kirwan, mayor in 1686; Dominick Browne, mayor in 1688; various O'Donnellans; Burkes; O'Briens of Clare; McDonnells, including Col Alexander McDonnell, mayor in 1690: the list could be extended for several pages.

From “The history and antiquities of the diocese of Kilmacduagh” by Jerome Fahey, p. 329:
“On the 11th of May 1697, the O’Shaughnessy estates were declared confiscated, and a formal Act of attainder and forfeiture was issued against Sir Roger O’Shaughnessy, lately deceased, and his son William. . . it shows clearly the vast extent of property of which those men were robbed in the name of law. Its extent was ascertained by an “Inquisition: held at Galway, under one Morley Sanders, on the 5th of September, in the eighth year of William the third’s reign. The residences of which he was deprived are mentioned as well as the lands. We also find the names of the various mortgagees: - Walter Taylor of Bally MacGrath (Castle Taylor). Bryen O’Briend, Dermot Tully, Turlogh O’Heyne, Charles O’Shaughnessy, and Dermot Cloran. This Dermot Cloran resided at Lissine, about two miles south of Gort, and was the family lawyer. Fortunately, some of his papers, which refer to the mortgages on the O’Shaughnessy espates of the period, are preserved in the appendices to Mr. Blake Forster’s work. (Irish Chieftain, p. 582)”

From same source above, p. 330:
Among the bonds in Cloran’s possession was one from a Protestant Williamite named Walter Taylor. Captain Roger O’Shaughnessy had purchased land called Carubesida from Taylor, who had bought if from a patentee. Taylor gave his bond to execute a conveyance of those lands to O’Shaughnessy, but, however, he did not do so, as Dermot Oge did not attend to the affair at the time or afterwards, being in a depressed state of mind on account of the loss of Aughrim and the fall of Limerick. The Williamites being victorious, Taylor dishonourably took possession of Carubesida. Dermot Oge feared to question his right to do so, lest Taylor might injure him in his endeavours to keep Lilline. Therefore Taylor got back the bond, and kept the land, without returning to OShaughnessy the purchase-money which he had received from his father. This dishonourable transaction on the part of Taylor is fully explained by Dermot Oge in the notes and memorandums he left on his death to his son, for O’Shaughnessy’s use. This transaction is referred to more in detail by Dermot Cloran in his memorandum drawn up for the guidance of William O’Shaughnessy.