Complex sentence: Areas occupied by USSR were annexed to Soviet territory, with the exception of area of Vilnius, which was transferred to Lithuania, although soon attached to USSR, when Lithuania became a Soviet republic.
Split into simpler sentences: Areas occupied by the Soviet Union were annexed to Soviet territory, with the exception of the Wilno/Vilnius region, which was transferred to the Republic of Lithuania. Lithuania itself was soon annexed by the Soviets and, including the contested Wilno area, became the Lithuanian Soviet Republic.