Kammala jumla mai zuwa: Iyalan Bačkis a Lithuania sun tsananta wa Soviets; ɗan'uwansa Juozas ya kasance
An tura shi zuwa Siberia a watan Yunin 1941 inda ya mutu bayan shekara guda. Gestapo ta kama Klimas a watan Satumbar 1943, wanda ya bar Bačkis babban jami'in diflomasiyya a Faransa. A wannan shekarar, Bačkis ya kare digirin digirgir a kan Concordat na Lithuania (wanda aka buga a Lithuanian a 2007; ). Bayan yaƙin, Faransa ba ta amince da ayyukan diflomasiyyar Lithuania, Latvia, ko Estonia ba, amma ta ba su damar yin aiki ba bisa ƙa'ida ba. Bačkis ya ci gaba da ilimantar da jami'ai daban-daban game da mamayar Lithuania da kuma matsa lamba don rashin amincewa da SSR na Lithuania don tabbatar da ci gaba da jihar. Ya kuma wallafa labaran labarai game da al'amuran Lithuania (ciki har da lambobi 33 na "Questions Lithuaniennes", lambobi 8 na "Bulletin Lithuanien", da littafin "Peuples opprimés. La tragédie des Etats Baltes"), ya taimaka wa 'yan gudun hijirar Lithuania, da dai sauransu. A cikin 1948, Bačkis ya yi hulɗa da Juozas Lukša, wani mai adawa da Soviet wanda ya yi nasarar tserewa daga Iron Curtain, kuma ya taimaka masa yaɗa bayanai game da gwagwarmayar soja. A cikin 1949, Kwamitin Kasashen Tsakiya da Gabashin Turai, wanda ɗan majalisar Burtaniya Harold Macmillan ke jagoranta kuma yana wakiltar ƙasashe daban-daban na Gabashin Gabas, Ƙungiyar Turai ta kafa. Bačkis ya zama mataimakin shugaban kwamitin a shekarar 1951. Ya kuma kasance wakilin Lithuania ga Tarayyar Tarayyar Tarayyar Turai, ya shiga Nouvelles équipes internationales (Sabuwar Ƙungiyoyin Ƙasashen Duniya), da kuma Majalisar Kasashen Turai. Bačkis ya kuma bukaci sake kafa Kwalejin Kimiyya ta Katolika ta Lithuania kuma ya gabatar da takardun bincike a cikin zamanta. A cikin 1950, Vatican ta ba shi lambar yabo ta St. Gregory the Great.