In 1443 the Butler–Talbot feud seemed to be dying down, but in 1444 it flared up again. The immediate cause of conflict was Thorndon's refusal to reappoint William Chevir, a key ally of Ormonde, as his deputy. Thorndon now abandoned any effort to mediate and declared himself to be firmly on the Talbot side. He produced a string of complaints against Ormonde and Chevir, covering a wide range of examples of corruption, bribery, maladministration, and disobedience to the Crown. Ormonde responded by calling a meeting of the Council at Drogheda, where he declared that Thorndon was deemed to have vacated his office, and accused him of treasonable conspiracy with the quarrelsome and litigious Thomas FitzGerald, Prior of the Order of St. John of Jerusalem at Kilmainham. Thorndon and Prior FitzGerald fled to England where they charged Ormonde with treason, and (rather curiously) with necromancy, but the Privy Council, which was only concerned to end the feud, was unsympathetic to their complaints. No action was taken against Ormonde, and the Prior was permanently deprived of office in 1447: the Council's proposal that the two men settle their differences through trial by combat was vetoed personally by King Henry VI, who persuaded them to agree to a truce. Thorndon, as far as is known, did not return to Ireland, although his later marriage to Jane d'Artois, widow of Lord Gormanston, suggests that he remained in contact with some of his former colleagues there. Despite his unhappy experiences in Ireland, it was clearly felt by the Crown that Thorndon had acquired useful knowledge of the governance of the country: in 1458 he was confirmed in office as Treasurer of Ireland. Unsurprisingly he preferred to appoint a deputy to act in his place. He retired to Northumberland in 1460, shortly before the downfall of the Lancastrian dynasty which he had served so long and loyally. The new Yorkist regime, which was generally in favour of reconciliation with its former opponents, left him in peace: whether he maintained contacts with the exiled Henry VI or his Queen, Margaret of Anjou, is unknown. During the brief Readeption of Henry VI in 1470-1 he seems to have played no political role, probably because of his great age. He died in August 1477, aged almost ninety. He married, sometime after 1450, when they were both rather advanced in years, Jane d'Artois, dowager Lady Gormanston; she was the daughter of the prominent Gascony-born military commander and landowner Sir Jenico d'Artois and his first wife Joan Taaffe, and widow of Christopher Preston, 3rd Baron Gormanston.