To escape the advancing Soviet troops, who he had reason to believe would arrest him due to his Belarusian political activities, Jan crossed the nearby border to Lithuania until the events of 1940.

The City of Vilnius returned to Lithuania shortly before the country was occupied by the Soviet Union, Jan Stankievič then left for East Prussia and made his way to German-occupied Warsaw which was becoming a magnet for a variety of refugees from other Soviet-occupied lands.

Convinced of the eventual defeat of the Nazi regime, they make connections with the Polish underground and its exiled government in London to influence the post-war outcomes in Eastern Europe.

During this time, Jan Stankievič's wife and 3 young sons moved to Prague in the now German-occupied Protectorate of Bohemia and Moravia to rejoin her extended family.

After the Germans launched a quickly successful surprise attack on their former ally, the Soviet Union, in June 1941, many of the refugees in Warsaw from formerly Soviet-occupied areas such as Vilnius and Minsk returned home, including Jan Stankievič.

However, by 1944, news of the approaching Soviet army caused Jan Stankievič to leave Prague for the American zone of occupation in the west where he eventually settled in Munich, Germany.