It seems most appropriate to allow Doyle to introduce our first question:

“And why, after all, would there be records? In the cities, security forces had sought to dismember guerrilla networks with maximum deniability. Death squads operated out of uniform, in unmarked vehicles, and the newspapers played along, reporting each fresh corpse as the work of ‘unidentified men in civilian clothing.’” – Kate Doyle

This is really a two-part question:

Why would the Secret Police insist on record keeping?
I suggest that while the records were “active,” they formed a vast, encompassing, and inescapable network of complicity. Everyone working for the Secret Police was involved, and their work was detailed with painstaking accuracy so nobody could deny their participation. This is pretty common to records of terror.
It follows that these records (again during their active phase) served as an instrument of terror even for those working within the Secret Police. Understanding complicity means that the individual Secret Police knew there was no escape. The vastness of the records creates an environment of inescapable awareness that those in power held every individual accountable. Put more simply, the vastness of the records prove the unlimited power of those in charge. Simply, there was no escape for those institutionalized into the torture and disappearanc of thousands.   

From the point of view of the archive, the Atrocity Files are fascinating because they highlight how records can be composed, preserved, and organized with a set of intentions and values that, in time, become oppositional to the values and purposes the same records assume when placed in new political circumstances?

Simply, records that were once the instrument of terror become, when discovered and introduced to the survivors of terror, essential memory in that the records are a form of posthumus resistance and perseverance. Remember, and as Doyle notes, all of Guatemala was a vast unmarked grave. Bones are anonymous. On an individual level, the records provide closure for individual families. Collectively, on a more macro view of an entire society recovering from the trauma of terror, these records in themselves become a monument to the eventual triumph over terror.

The life cycle of these records portrays a remarkable process of Truth and Reconciliation. 

Probably pretty self-evident by this point: past is prologue. Tragically it seems unlikely that the world will stop producing horrific political regimes. And, equally tragic, these regimes are (in general) not stupid in their commitment of autorities. Even totalitarian regimes are aware of historical examples for the exercising of terror. Record keeping is part of that process.