After the formation of the Lithuanian Soviet Socialist Republic in July 1940, Gens was fired from his job. He was unable to secure a work permit nor was he allowed to continue to live in Kaunas. He went to live with his brother, Solomon, in Vilnius, and although Gens was on a list to be sent to Soviet labor camps, he managed to secure an unregistered job at the Vilnius health department through an old military colleague, Colonel Juozas Ūsas. Gens was not on the official payroll, which meant that the political officer attached to the hospital did not need to be informed of his employment. During June 1941, when thousands of the Lithuanian elites were exiled to Siberia, Gens remained in hiding and was not deported.