Information about Koffler and his family’s fate in this period, and their end, is not consistent. Maciej Gołąb offers as many as five hypotheses concerning the composer’s death, varying in probability. None of them can be confirmed for lack of direct sources. The following seems to have been the most likely course of events.
Koffler fled Lwów and came to Wieliczka, where no ghetto was formally established (unlike e.g. in Kraków). For this reason, Jews from Kraków and its environs flocked to Wieliczka in an attempt to escape being locked in a Jewish district. Most of the newcomers were representatives of the Jewish intelligentsia, including Henryk Apte and his family. Apte was a co-founder and active member of the Jewish Music Society in Kraków. His son Ryszard had been Koffler’s pupil at the PTM Conservatoire in Lwów. It is possible that the Kofflers came from Lviv following the Apte family.
When the Jewish community realised that they would be deported (since the Judenrat was ordered to pay tribute), many Jews fled Wieliczka. The Kofflers also probably did so, thus avoiding the deportation, which took place on 28 August 1942.
After leaving Wieliczka, the most likely trail leads to the environs of Krosno. Koffler’s sister-in-law Gizela Hercholorfer admitted in a letter to the editors of Życie Warszawy daily (1 July 1987) that she had met Józef in 1942 at Krosno railway station. He was supposedly hiding in Krościenko Wyżne, where he had a pupil, probably the local parish organist Władysław Piękoś. According to Maciej Gołąb, the Kofflers and their son may also later have found shelter at a different address in the village of Krościenko Niżne, until in 1943 or (the spring of) 1944 they were all captured and murdered by the Germans at an unknown place and in unknown circumstances.