Complex sentence: The Counter-Reformation swept through most of Slovenia, excluding easternmost regions (including Prekmurje) ruled by Hungarian nobles, who themselves often happened to be Calvinist and did not seek to extinguish Lutheranism, which became the preferred confession among Slovenes.
Split into simpler sentences: The Counter-Reformation swept through most of Slovenia, excluding easternmost regions (including Prekmurje) which were ruled by Hungarian nobles, who themselves often happened to be Calvinist. They did not seek to extinguish Lutheranism, which became the preferred confession among Slovenes.