First of all, the Holy Roman Empire wasn't a "German Holy Roman Empire". The English Wikipedia, and unfortunately also some Anglo-American historians, tend to be more inaccurate about it than German historians. It included West Slavs, South Slavs, Gallo-Romans, Italians and many different German peoples and was reigned by princes of almost all of these ethnicities. The suffix "Deutscher Nation" / "of German Nation" wasn't used until the de facto loss of Italy, the Ottoman threat in the east and the Burgundian / French threat in the west.

German settlers came to some of the Slavic and Baltic regions especially in the High Middle Ages and in the end formed majorities or assimilated the majority in regions like Brandenburg, Upper Saxony, Lower Silesia, Pomerania or Prussia. In other regions like Poland or Russia, many German settlers on the other hand were assimilated themselves. The image drawn by 19th century historians of a "German colonization in Eastern Europe" that suggests German supremacy in this process unfortunately still exists - it is however hardly accurate. Slavic people contributed to the "colonization" as well. Nationalities usually did not play that much of a role, neither for the peasants who didn't see much of the world anyway, nor for the church and the aristocratic administration, where Latin was still widely in use. It is a modern misconception to think that medieval monarchs had the legislative power to change a people's civil law system (yes, right, a people's civil law system, because law was applicable to people instead of a territory). That being said, if a monarch spoke German or French played no role for the people as long as they shared or at least tolerated their religion.

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The lands of the Bohemian crown however can't be compared to the other Slavic-German mixed territories in the east of the Empire. The main difference was Bohemia's power.

From the 9th to the early 14th century, Bohemia was ruled by the Přemyslids. Their power was unique among the Imperial princes, and so was their prestige since Bohemia was granted the rank of a hereditable Kingdom by Philip of Swabia in 1198. During the Interregnum (1254-1273), when the Hohenstaufen Kings and Emperors died out (or rather, were eradicated by the Popes) and there was no one who had the power to restrict King Ottokar II Přemysl of Bohemia, he was able to expand his rule from Bohemia through to the Adriatic Sea. The German princes began to regard him in his powerful position with distrust. In the end, the new Roman King - a 60 year old Swabian (today Swiss) Count with few own hereditable territories called Rudolf of Habsburg - was able to form an alliance against him, won in the Battle on the Marchfeld in 1278 and gave Austria to his own son, Albert I.

Soon after the death of the last male Přemyslid King Wenceslaus III in 1306, John of Luxembourg, the son of Emperor Henry VII, who was later known as "John the Blind" married Wenceslaus' sister Elizabeth and became the new King. This made Bohemia end up with a King with a cultural identity that was entirely unknown to the Bohemian nobles. His culture, however, cannot be described as German either.

Luxembourg was a typical western border territory of the Holy Roman Empire. Although it was legally part of the Holy Roman Empire, the counts established close ties to the French Kings and pledged them their allegiance. Henry V of Luxembourg followed Saint Louis on the 7th Crusade and survived. The prestige gained from this is part of the root of the later Luxembourgian emperorship and the Luxembourgian friendship to the Valois. Multiple Luxembourgian counts - including John - grew up in Paris at least for a while, where they experienced sophisticated education and the French values of chivalry.

Calling him "King Stranger", the Bohemian nobles never got to like John very much. He himself never bothered to learn Czech and wasn't even present in Prague that often. How the things were done in his own kingdom, its traditions and uniquenesses went over his head. John's attempts to establish a culture of chivalry (for example through knights tournaments) in Bohemia didn't work at all. It is recorded that the Luxembourgian Kings were exhorted to appoint Bohemians as their advisors and that the strong nobles who owned many allods strongly wished to delimitate the influence of persons from the rest of the Empire. However, the Bohemian nobles of German origin also seem to have had the same strong exclusive Bohemian identity.

John's son Wenceslaus, who was later renamed after his godfather King Charles IV of France and became the Emperor Charles IV, was different. He saw his blind father die an evitable chivalric death in the Battle of Crécy in 1346 (where John led a wing, in case you'd like to know how leading an army as a blind man works: It didn't) and felt few to no thirst for adventures since then. Charles IV never strained Bohemia with the burdens of war, spoke Czech fluently and led Bohemia, after the black death ended, into a literally golden epoche - Prague's golden roofs and its nickname "The Golden City" originate from these days. When he was absent from Prague, Charles was usually not that far away in Nuremburg, the most important Imperial City of these days, that he visited over 70 times. Charles' Golden Bull (1356) that is considered the constitution of the Holy Roman Empire, mentions that the sons of Prince Electors are supposed to learn Czech. He also founded the first university in the transalpine Empire in Prague in 1348. It became a cultural center for both the German and Czech culture.

The conflicts between Czechs and Germans escalated during the reign of Wenceslaus IV "the Lazy" (1378-1419). The Hussites, a reformation movement named after its initiator Jan Hus, demanded many things that are similar to what Martin Luther would demand a century later, for example the restauration of the poverty of the church and the right to preach for laymen. After Hus was burned as a heathen at the Council of Constance in 1415, the conflicts escalated. Hus was granted safe conduct by the Roman King Sigismund of Luxembourg, the successor to the Bohemian throne. Him being killed was regarded as a betrayal by the Hussites, even though it must have been known that safe conduct to the Council doesn't equal an amnesty if the verdict of the Council was a death sentence. Sigismund himself had no benefit from killing Hus and weakening his position in Bohemia. In fact, he couldn't take over the reign in his Kingdom until 1436, because the Hussites rioted and devastated many bordering lands. In these days, many Catholics - which often equaled Germans - were expelled. After the peace, rulers for a very long time had to make compromises with the powerful Hussite / Protestant Bohemian nobles and the reign was somewhat shared until the age of absolutism.

As for the "Sudetenland": This is a modern artificial term that was invented (or popularized) after the First World War for the entirety of the territorial claims of the Republic of German-Austria ("Republik Deutschösterreich") to the old lands of the Bohemian crown. Austria wished for the people to decide where they would belong to through a plebiscite (which never happened); the "Sudetenland" is the territory where a decision in favor of Austria would have been probable because there used to live more "Germans" than "Czechs". Nationalism is arbitrary, complicated and inconsitent. There was never a linguistic or cultural border between Czechs and Germans. In reality, almost all cities and towns had mixed populations of Germans, Czechs, Jews, and many people had ancestors of more than one of these groups after one thousand years of living side by side. In 1904, when the first German football championship ended, the final was between a team from Leipzig and a team of Jews from Prague; they naturally considered themselves German. Germans from the "Sudetenland" never played a bigger role in the history of the administration of Bohemia than for example the German upperclass in Prague.

Literature: Jörg K. Hoensch: Die Luxemburger; Norman Davies: Verschwundene Reiche; Peter Oestmann: Wege zur Rechtsgeschichte (and more I'd have to look up)

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I'm sure a lot more can be said, about the Habsburgs' rule and especially the Thirty Years' War, but I'll leave it at that as I think my points have been made.