This concept is very clever, the story is intriguing and your writing really conveys the feeling of the different types of documents and the characters' personalities. There is something really refreshing about the switch in styles (going from letter form to interview transcriptions etc).
I can't help but think Choicescript is the wrong medium for this kind of thing, though. I can imagine it being great in a more traditional style of IF, where the player actually types in text commands to search the files, like a cmd prompt:
Your search yielded 3 results
As it is right now, I feel a little disconnected from the game. I think precisely because of the reason above, that I'm not actually searching through files myself, there is just a list of search terms that I can pick from... I'm sure the path I take through the files will have some consequence (or I hope it will), but it doesn't feel that way. Feels like I'm just clicking through the files at half-random and that they're presented in a sequential, linear order, so my choices don't really matter.
Ideas for improvement
If you really want to stick with doing it in ChoiceScript, I have a few ideas you might want to consider. (Not sure if any of this could work in this case, I'll let you be the judge of that.)
The "new search" menu bugs me because if I'm actually searching for documents containing a word like "Cardinale", I would expect it to show me a list of several documents that contain my query (as above). But I'm immediately shown a letter or other document. Instead of or after a search menu, you could have a list of files to pick, even maybe files named like files. For example: "letter_cardinal_thayer1993.txt" or "CIA_Transcript_Hartley.pdf".
Also, I noticed that a couple times I used a search term and the document it pulled up had none of the keywords in it. For example, the second "Xinnabela" choice pulls up the "archaeological excavation report filed by Dr. Thayer, L., PhD", which makes no mention of that word at all (which makes me wonder why it would come up as a result at all). Similarly, "Marco incident" pulls up the "from the CIA interview of Hartley, M" document, which made no mention of the keywords "Marco" or "incident".
I get that you can't make a list of every single file pertaining to a search query because you need to control the story progression. Which brings me to my next point:
There needs to be some sort of progress tracking or some sort of reason I can't access the latest, most illuminating files right from the start. I would suggest something like a "X% decrypted" stat on the stats page, you start at 1% decrypted, and every time you open a file it increases the decrypted stat, which then allows you access to new files. That would explain why a search term might not pull up all the pertinent documents from the start. If I pick "Thayer" in "Search Now", there could be a list of several documents, and the ones you don't want the player to see till later could be unselectable and marked as such: "letter_thayer.txt (9% decrypted)" That would make me feel like I have something to work towards, you know?
There could also be some sort of countdown of the time you have left to solve the case. Or just regular count of how many "hours" you spent searching the documents. That could work as a motivator to not waste time examining less helpful documents that you could bypass. It could also be used to determine the endings you get, like if you manage to save Thayer's life (if that's one of the ultimate goals). A simple count of the number of documents the player has read could also do the trick.
Another way to help give the player a feeling of progression would be to use achievements. Right now, I have no idea if what I'm reading is just general documents that basically everyone reads in every playthrough, or if I'm on a branch, a path that leads somewhere that I wouldn't have gone if I had chosen another option. If an achievement pops up says "You discovered X", then I'll know I discovered something cool/interesting, maybe unique because of my choices, and that I'm making progress.
So that's it from me, sorry for the wall of text, I hope I expressed myself ok and it's not too much of a garbled mess. This is a great, unique WiP, I wish more people would share their thoughts about it. I wish you good luck, I'll be keeping my eye on this one =)