I'm afraid that this is incredibly vague. What you're asking about is historiography, the study of the study of history. Given that people have been studying the past since at least the ancient Greeks, yes, there have been quite a few changes in the field in the last ~3000 years. I think you may need to refine your question a bit.

I believe the Rosetta Stone could be what your looking for: The Demontic (a modern Egyptian way of writing) script was included with Ancient Egyptian hieroglyphs, which their meanings were rather ambiguous before it's discovery. With it, they uncovered what some hieroglyphs meant, or at least a very good impression, and helped us to understand so much about Ancient Egypt, especially in a more detailed format.

http://discoveringegypt.com/egyptian-video-documentaries/mystery-of-the-rosetta-stone/

I can help expand on helping you understand your own question a little bit. Again, as has been said, the "history of history" is historiography and it forms a small but significant portion of a historian's work: when researching a subject, it's important for a historian to understand what approaches to the subject have been made. A historical thesis would almost always include a literature review in which the historian would go over previous work done on the topic. The goal of this is often to establish why new work is necessary.

The major way historians innovate is to change the way they encounter primary sources, the kinds of primary sources they might find interesting or take into account the context of the primary sources.

The History of Science is my field and so I'm most familiar with the historiography of that field. Very broadly speaking, you could say that the history of science began being focused largely on individual scientists and researchers. Histories were biographies either of one individual or a series. Moreover, histories of science were of certain types of individuals, 'heroes' of science, often national heroes.

As the History of Science has developed, it has broadened and deepened. Historians of Science (and I assume this is general to all fields of history) have questioned the standard narratives of previous generations and stepped away from writing biographies of mostly men working as heroic individuals. More sociological approaches have been common since the 1960s. These approaches involve the community and the society of the scientists, and include looking at workshops, assistants, friends, collaborations, interactions with other fields and such topics.

For example, the narrative Isaac Newton as physicist and mathematician has been broadened to investigate Isaac Newton's other interests (the occult, magic, alchemy) and his other roles (as head of the Royal Mint). Other histories might avoid the typical 'greats' entirely as unnecessary to crucial stories-- instead of a book on the invention of the steam engine (although those obviously still exist, but in a developed form) you might also have one that looks at the interactions between doctors and patients, or one that looks at the role of managing risk in development, or one that examines the practical problem of time synchronization to the development of the very theoretical idea of relativity. (Note: links to books are not necessarily endorsements of these ideas, meehee).

This (incredibly broad generalisation of a) innovation in history has made a significant difference in our understanding of science, medicine, technology, invention, research and innovation. For one, we understand that scientists in the past, as today, were typically not individuals having genius ideas alone in laboratories. They (and science done at a certain place) were products of their environment and worked with a deeply connected community in interesting and complicated ways.

Maybe try narrowing down this question - but I will answer as I please. There is constant innovation in how we study history. Currently, I work as an investigative archaeologist (super liberal term because there is no other term). My job is to reconstruct Egyptian 19th Dynasty tombs in the Memphite necropolis of Saqqara; based on archaeological findings, extensive research and my knowledge of the architecture, I am able to create 3D digital models. I am working with the team behind Digital Karnak which is mostly finished but ours is still very much under construction.

This season, I will be on site digging in a necropolis in Spain and will be using GIS systems to map the necropolis and its burial, as well as photogrammetry to record the site at every stage of the dig. Photogrammetry is ridiculously easy and so helpful when digging on-site.