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During the 2nd World War’s Sonderaktion Krakau operation, Konopczyński was arrested by the Germans and sent to Sachsenhausen concentration camp. After returning to Kraków, he committed himself in underground educational activities of the Jagiellonian University and became the head of the history faculty. Throughout the period of German occupation, he lived in his family’s manor house at Młynik near Ojców, where from 1944 he was hiding a Jewish family. He wrote many important scientific worksduring the war, and only part of them was published, the rest remained in typescript in his family collection. In the years 1940–1942, Konopczyński prepared a two-volume work entitled Piłsudski a Polska and simultaneously drafted the Polish history of the years 1918–1939. Then he wrote Konfederacje w rozwoju dziejowym, which was not published at all and until today remains in typescript. The reason it was not published was that his name was on the blacklist of the censorship in the Polish People’s Republic. His next important work was a methodology manual Historyka, which because of the abovementioned censorship at that time was not published as well. Only 70 years after the work had been finished by the author it was published by Maciej Janowski, with his detailed introduction, under the imprint of the Institute of the History of Science. After finishing this work, Konopczyński got down to writing a biography of his long-standing friend, Stefan Surzycki (the typescript of the unpublished work is in the PSB editorial office). Next, he wrote a monograph entitled Pierwszy rozbiór Polski, which was published only after 60 years, compiled by Zofia Zielińska and thanks to the efforts made by the “Arcana” publisher. An academic book entitled Kiedy nami rządziły kobiety was devoted to the times of the reign of Stanislaus II and the Confederacy of Bar. It was published only in 1960 in London. The third trend in his writing was represented by the works: Fryderyk Wielki a Polska (1947) and Kwestia bałtycka do XX wieku (1947). After completing his work on Kwestia bałtycka, Konopoczyński got down to writing Dzieje Inflant, i.e. the history of three nations: Latvians, Estonians and Baltic Germans, addressed to the general public. Currently, this typescript is being prepared for publishing by the Center for Political Thought in Kraków. Konopoczyński was simultaneously writing numerous minor sketches and syntheses for the general public, e.g. Krótki zarys dziejów Polski, Polska w dobie pierwszego rozbioru and biographies of Stanisław Dunin Karwicki, Józef Sawa Caliński, Andrzej Zamoyski and Ferdynand Nax. Only part of those works went to print. Among the works most vital to the science were: Chronologia sejmów polskich 1493–1793 (1948) and Reforma elekcji – czy naprawa Rzeczypospolitej. (Wybór źródeł 1630–2) (1949).