This paper sheds light on the fate of two very important 15th-century paintings, originally part of the Dukes of Urbino’s picture gallery, the ‘Flagellation of Christ’ by Piero della Francesca and the so-called ‘Ideal City’. The paintings have in common the dynastic significance they assumed in the late 16th and early 17th century in the eyes of intellectuals at the court of Francesco Maria II della Rovere, starting with Bernardino Baldi, abbot of Guastalla, with the full approval of the last duke of Urbino. In one of the three figures on the right of the ‘Flagellation’, the original portrait of Oddantonio da Montefeltro was identified, albeit arbitrarily, and copies and variants were taken from it. Oddantonio, for whom an arduous historiographical rehabilitation was attempted after the long damnatio memoriae imposed by Federico da Montefeltro, had in fact been the first duke of Urbino, recognized by the Church but also by the Empire. The panel was therefore seen as a kind of certificate of historical and dynastic value to be used at the time of the duchy’s imminent annexation by the Papal States. The architectural ‘scene’ or perspective was instead wrongly interpreted as a model of Federico’s first mausoleum designed within the palace and was therefore destined for the church of the Poor Clares, which during the years of Francesco Maria II della Rovere had become the burial place of the dukes themselves. Precisely because of this ideal but also implicitly political value that the two paintings had taken on, in all probability the last duke of Urbino wanted to bind them respectively to the Duomo and to the church of Santa Chiara, so as to prevent the two panels from being transferred, like the rest of the collection, to the Florentine galleries following the marriage in 1634 between Vittoria della Rovere and Ferdinando II de’ Medici.