When I work on stories, I generate a ton of notes. I find, though, that a lot of these notes are transient things that I don't need a few days later. And I typically want to pare down the notes that I'm referring to while I work on a draft, because if the file of notes is too long, it's hard to use. Plus, as things change, notes become out of date.
Also, a lot of my notes are simply lists of ideas: as soon as I get stuck on 'what's a good way for CactusMan to defeat the Crimson Tide's Blood Tank', I start a list.
(He sticks it to 'em though, of course. That's what CactusMan does.)
But it's hard to delete notes, as I worry that I'll need them later.
In recent projects, what I do to pare things down is throw the notes I'm done with in an archive file. That way they're not deleted and if I really need them, I can go find them.
I almost never do; they just hang out in the archive notes file forever. But that's okay. Having that reduces my inhibitions about throwing things out and cleaning up, and so I can clean out the cruft more easily.