The whole of the building was rebuilt in the second half of the 11th century, in the period of High Romanesque, and inaugurated in 1086 by the future Pope Urban II.
Roger as a secular ruler seemed a reliable ally, since he was merely a vassal of his kinsman the Count of Apulia, himself a vassal of Rome, so it seemed safe at the time for Urban to give him these extraordinary powers, which were later to lead to bitter confrontations with Roger I's Hohenstaufen heirs.
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The origins of the investiture controversy, according to Jay Rubenstein started with Pope Urban II whose central problem was a war against Henry IV, Holy Roman Emperor (1056-1106).
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In accordance with this last policy, the marriage of the Countess Matilda of Tuscany with Guelph of Bavaria was promoted; Prince Conrad of Italy was assisted in his rebellion against his father and crowned King of the Romans at Milan in 1093; and Henry IV's wife, the Empress (Adelaide), was encouraged in her charges of sexual coercion against her husband.
The war was finally resolved by the mediation of Pope Urban II and the award of Taranto and other possessions to Bohemund.
However, in Bari other relics of the saint were already put in 1089, they were laid in the tomb, by Pope Urban II in person.
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When Pope Urban II, the greatest of the Gregorian reformers after Gregory, travelled through Languedoc and Provence, visiting Montpellier, Nîmes, Saint-Gilles, Tarascon, Avignon, Aix, Cavaillon, and other cities, preaching the First Crusade at the Council of Clermont in 1095, he had to avoid Arles, where the deposed bishop was still in power.
Beside obtaining from the French legislature an appropriation of two millions of francs for the restoration of Reims cathedral, he secured for the Trappists the ancient Abbey of Igny, and for the Oratorians the priory of Binson, and erected at Châtillon the colossal statue of Pope Urban II, whose cultus he had promoted in Rome.
Hugh's relationship to Ferdinand I and Alphonso VI of León and Castile, as well as his influence upon Pope Urban II, who had been prior at Cluny under Hugh, made Hugh one of the most powerful and influential figures of the late 11th century.
Herbert de Losinga was appointed a papal legate in 1093 by Pope Urban II to investigate the matter of Thomas' profession of obedience to Lanfranc.
St-Calais managed the king's case against Anselm at Rockingham in 1095, when Anselm wished to go to receive his pallium from Pope Urban II.