The Operative: No One Lives Forever

As in most levels, there are two different "sets" of Intelligence Item locations. It seems that one of them is missing one of the items (which is your case), either that or it's the best well hidden item in the entire game.

The solution is to make a manual save just BEFORE entering the elevator which finishes the level in "Safecracker, Scene 5". Then, when you start "Safecracker, Scene 6" look in the first room to your right which is after the large room with the two guards talking about "Stinks". If you see a letter sitting on a table in that room that's the wrong set, so reload from the manual save and try again. The letter should be in its alternate location which is in the same room but on the second floor sitting on a chair. This way you'll surely find the folder on the desk you've been missing.

Hope that helps, cya!