World War II again challenged Bogatyrets' national affiliations, leading him to support reunification with the Russian Orthodox Church. He stayed behind in Soviet territory after the occupation of northern Bukovina but was eventually forced into exile. He lived in Nazi Germany and Romania to 1941, when the German–led invasion allowed him back to Cernăuți (Chernivtsi). For three years, he assisted Metropolitan Tit Simedrea and took over effective leadership of the Diocese when Simedrea left Bukovina. He joined the Ukrainian Exarchate in late 1944, welcoming back the Soviets, but was marginalized from 1949. His final work was as a historiographer of the regional church through its various administrative avatars.