During the Khmelnytsky Uprising (1648–1649) the Cossacks plundered Kaidanover's possessions, his valuable library and his manuscripts among them, and killed his two little daughters, and he arrived in Moravia an impoverished fugitive. He was elected rabbi successively of Langenlois in Lower Austria, Nikolsburg, Glogau, Furth, and Frankfurt am Main, and then returned to Poland, in 1671 to become the rabbi of Cracow a position he held until his death on December 1, 1676 while attending the Vaad HaGalil of Krakow that took place in Chmielnik.