Bačkis' family in Lithuania was persecuted by the Soviets; his brother Juozas was deported to Siberia in June 1941 where he died a year later. Klimas was arrested by Gestapo in September 1943 which left Bačkis senior diplomat in France. The same year, Bačkis defended his PhD thesis on the Lithuanian Concordat (published in Lithuanian in 2007; ). After the war, France did not officially recognize Lithuanian, Latvian, or Estonian diplomatic services, but allowed them to function unofficially. Bačkis continued to educate various officials about Lithuania's occupation and lobby for non-recognition of the Lithuanian SSR to ensure state continuity. He also published informational bulletins on Lithuanian affairs (including 33 issues of "Questions Lithuaniennes", 8 issues of "Bulletin Lithuanien", and book "Peuples opprimés. La tragédie des Etats Baltes"), helped Lithuanian refugees, etc. In 1948, Bačkis made contacts with Juozas Lukša, an anti-Soviet partisan who managed to escape the Iron Curtain, and helped him spread information about the armed struggle. In 1949, Committee on Central and Eastern European Countries, chaired by British MP Harold Macmillan and representing various Eastern Bloc nations, was established by the European Movement. Bačkis became vice-chairman of the Committee in 1951. He was also a Lithuanian representative to the Union of European Federalists, joined the Nouvelles équipes internationales (New International Teams), and Assembly of Captive European Nations. Bačkis also urged reestablishment of the Lithuanian Catholic Academy of Science and actively presented research papers in its sessions. In 1950, he was awarded the Order of St. Gregory the Great by the Vatican.