This territory was a part of Poland until 1772 (the First Partition of Poland) and was in 1921 returned to Poland after the Versailles Treaty. The German inhabitants of this part of Poland felt not welcome, because Germany was one of the neighbouring countries that was seen by Poland as wanting to wipe out Poland from the map of Europe and the ethnic Germans were quite often seen as just members of the fifth column.
Many former German citizens, now only ethnic Germans, had already resorted to leave the German provinces that fell to Poland after WWI, partially as effect of German propaganda which thought that without German lawyers and doctors Poland will be forced into chaos. After the death of the
moderate leader of Poland Jozef Pilsudski in 1935, Polish nationalism,
supported by the Catholic church, flared.
A number of ethnic Germans were collected by the Polish authorities according to already established lists from of a number of cities and towns and sent on a march, herded from town to town. German sources claim that many of them were murdered including many pastors, precisely because they were now the 'official link' remaining to the ethnic Germans. It's hard to say how many Germans died during such marches; German historians claim the number as high as 1700 and attributes it mainly to Polish atrocities, but Polish side points that since Germans were marching during war, most of losses should be attributed to war conditions, especially since many German witnesses confirm, that columns were sometimes attacked by Luftwaffe (which strafed all civilians on the roads) and artillery.
Most controversial is case of Bydgoszcz events in September the 3rd. Polish witnesses testified that early that day Polish army withdrawing via Bydgoszcz was attacked by diversants; someone was shooting at soldiers and civilians from roofs and church towers. The fact of shooting is confirmed by some German witnesses, who however guessed that it was Polish provocation. There is no proof however that such diversion had place, no preserved documents, and German historians generally take whole fact of diversion as phantasy.
Whenever it was or not, Polish soldiers were convinced that German diversants were shooting at them and started to search the houses. In the hot hours in improvised military trials died unknown number of Germans, vast majority of them probably innocent. The scale fo the event is controversial. De Zayas estimates it for 2000; Hugo Rasmus compared Bydgoszcz address books and data for population for 1939 with Nazi lists of supposed victims and found 358 persons known from name who died that day in Bydgoszcz. Most of them are female and children. Jastrzebski, Polish historian, initially doubting in the scale of event, now is backing the Hugo Rasmus' number, thinking that Polish official government was unable to control the mob and sanctioned later what was in fact lynch.
Initially Nazis were claiming that 5000 germans died in Poland in September 1939. Later they inflated that number in 1940 to 58.000, and Hitler personally raised that number to over 60.000. De Zayas now estimates "conservatively" that number for 5.000. Although many of those killed were victims of the war conditions (many Germans were drafted to Polish army for example, cities were bombed by Luftwaffe and artillery, civilians on the roads were strafed), it's without doubt that some Germans were victims of local acts of violance, of which Bydgoszcz was most known example.
There are also Polish claims of German atrocities against Poles in Bydgoszcz, cited in the evidence given to the War Crimes Tribunals. A document produced by the Polish authorities claims that:
Source: Nuremberg Trial Proceedings. Vol. 9, day 88, Friday, 22 March 1946
Literature: Dywersja czy masakra? Włodzimierz Jastrzębski, Gdańsk 1988.Claims of Polish atrocities against Germans
The numbers quoted in document are now usually lowered to 20 to 40 Polish soldiers killed in Bydgoszcz at September the first, and in whole about 13.000 inhabitants of Bydgoszcz murdered during the war.