You are not distinguishing between the city and the surrounding region. Your people were from what was the Wilno region, not from the city itself. The city itself is indeed known as Vilnius these days and is in Lithuania, but at the time you speak of it was in Poland. It has also been in Russia in the past.

Border changes in that general area were common. By the time my grandparents (born at the end of the 19th century) turned 50, their native villages had been in two different guberniyas of the Russian Empire (Minsk and Wilno) and three different countries (Russia, Poland, and Belarus)!

When you refer to the Russians taking over the area, do you mean the Soviets? (Not all Russians were Soviets and not all Soviets were Russians. Just sayin'.)