One of my favorite examples of this is the understanding of medieval heresy. Many medieval inquisition records talk about most heretics as dualists, meaning (more or less) that they believe in a good god and an evil god who are equally powerful forces in the universe. For centuries, this was basically the general understanding of medieval heresy.

Over the past century or so, however, scholars (Carlo Ginzburg and others) have separated the heretics' own statements from those of the church, and found that very few of them actually made dualistic statements-- they were an ideologically-diverse group, but the church often tried to fit their statements into known heretical patterns.

In Ottoman history, the biggest example of this is the demise of the Decline Thesis. Historians of the mid-twentieth century understood as fact that after Suleiman the Magnificent died in 1566, the empire started to stagnate and decline until it came to an end after World War I. Ever since the '80s this has come under increasing criticism and nowadays basically no academic historian believes in it any longer, instead they view the empire after Suleiman as having entered a period of transformation which was neither inherently positive or negative, and emphasize the Ottomans' continued strengths into the seventeenth and eighteenth centuries, as well as the success of the reforms of the nineteenth.