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I have always considered this scenario very unlikely, as the Habsburgs were emperors in the Holy Roman Empire. But when I read more about it, I get the impression that the Protestants before the 30 years war were in a clear majority not only in the HRE, but even within the Habsburg lands that belonged to the Austrian branch of the family. It was only gradually, because of the Counterreformation, that these areas again became majority Catholic. Ferdinand I and Maximilian II were quite moderate in their reaction to Protestantism, as they had to react to the Turkish threat. If the Habsburgs had sided with the Protestants, all the secular electors would have been Protestant. Sure, the idea of a Protestant emperor would conflict with the ideology of a Holy Roman Emperor, but this ideology could be changed if it was deemed necessary.

So why would the Habsburg choose to do this. The main reason would be that Protestants were already in a majority. "If you cannot beat them, join them".

Of course, such a scenario would change the reaction of France. In OTL, France sided with the Protestants in Germany, even though the French king and the majority of his subjects were Catholics. If the Austrian Habsburgs turned Protestants. I would assume that France would have supported the remaining Catholics. This would also cut the ties between the two branches of the Habsburg family.
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