The numbers seem to refer to search terms, not necessarily the number of documents. If you want to make sure, try checking every possible search term. There are some hyphenated words that you’ll need to type into the search bar, clicking the word won’t work because it’ll only search for the half you clicked on.
edit: Nevermind, I see what you mean now about the ##/49 at the top of the archive. I’m still at 46/49 even though I searched for everything from the ones I have. I’ll need to try typing in a few things and see what works.
edit 2: I had to check the game files, but the last three documents can’t currently be found by searching, they’re not in the top three results for any of their search terms. One of them seems kind of redundant, one of them is a part 2, and one of them directly states a motivation that you probably already guessed if you finsihed everything.