During the most troubled years of the Ottoman - Austrian war, 1664–1669, he took refuge in the villages of Barbullush and Rjoll near Shkodra. A cave near Rjoll, in which he took refuge, still bears his name. Eventually, he was captured by the Ottomans and imprisoned in the fort of Shkodër. The bishop of Durrës, Shtjëfen Gaspëri later reported to the Propaganda Fide that he was rescued by the brothers Pepë and Nikollë Kastori. In 1677, he succeeded his uncle as Archbishop of Skopje and Administrator of Roman Catholic parishes in the Kingdom of Serbia. His religious zeal and patriotic fervour kept him at odds with Ottoman forces, and in the atmosphere of war and confusion which reigned, he was obliged to flee to Ragusa, from where he continued on to Venice and Padua, taking his manuscripts with him. In Padua he was cordially received by Cardinal Gregorio Barbarigo, Bishop of Padua at that time, whom he had served in Rome. Cardinal Barbarigo was responsible for the church affairs in the East and as such he had a keen interest in the cultures of the Levant, including Albania. The cardinal had also founded a printing press in Padua, the "Tipografia del Seminario", which served the needs of oriental languages and had fonts for Hebrew, Arabic and Armenian. Barbarigo was thus well disposed, willing and able to assist Bogdani in the latter's historic undertaking.