All historians are shaped by the archives themselves and the sources that have come to be contained in them. It used to be that archives were seen as untouched mines that could be exploited by a historian for pure information about the past, but archives are not really thought about like that any more. Instead, we know that archives were all subject to all sorts of complex processes (which are often problematic in many ways) that make them flawed.

There are so many examples in colonial Latin American history that I'm not even sure where to begin. In colonial Latin America, entire archives have been lost to fire, war, earthquakes, hurricanes, difficult climates, and theft. Many geographic areas have just a sliver of what historical information might have otherwise been available. For example, the colonial Inquisition records from Peru are now lost. Inquisition records are incredibly interesting sources used by countless early modern historians because they record the voices, folk beliefs, marriage practices, and sexual behavior of many non-elite people. In Peru, historians can't write the same kind of social histories about non-elite individuals that they can in Mexico, Spain, Italy, and Portugal. Fortunately, the summaries of many of Inquisition cases have survived, so although the full cases are lost, historians do have some records to go off of. However, the summary now inordinately shapes what historians can know about the past. Was the summary good? Bad? Incomplete? Who made the summary? What did the interrogations or witness statements of the full case contain? Were those accurately summarized or summarized at all? Did they leave out any key details? Such questions are sadly unanswerable.

The circumstances that led to the creation of sources themselves also change what we know about the past. Kathryn Burns wrote a famous book called Into the Archive, in which she explored the scribal practices of colonial notaries in Peru. Almost all documents used by colonial Latin American historians are notary documents, whether they are court documents, royal documents, royal proclamations, laws, bills, contracts, shipping logs, account books, slave sales, wills, land sales, and so on. Burns revealed that power relations existed between the notaries and the public, that local struggles affected the content of sources themselves, and that individual men and women at the time used notaries in specific ways to benefit their own lives. What this means is that sources previously thought to be "objective" have actually been shaped and mediated by all sorts of (largely) invisible hands BEFORE they even entered the archive. Centuries later, historians work with these archival materials to find information about those same people, and so their findings are shaped by the layers of power, local struggles, and individual strategies that led the documents to be created in the first place.

And of course language and accessibility affected our knowledge of the past, as you mention in your example. It is not a coincidence that the most famous sources from the colonial period continue to unduly shape how we think about the past. For example, the chronicles written by conquistadors are the dominant way that we know about the Spanish invasions of indigenous societies in the sixteenth and seventeenth centuries. These accounts of the invasions were written by the conquistadors themselves in Spanish (many quickly being transcribed and translated into other languages). Their stories intentionally spun the events in all sorts of ways, usually benefiting the conquistador who told the story. So much of the "what really happened" was never written down and thus lost forever. Obscure archival manuscripts written by not-so-famous conquistadores and sources in indigenous languages have only recently started being explored. You won't be surprised to learn that the accounts they provide, though still biased and written in their own self-interests, often tell remarkably different stories about the Spanish "Conquest."