I personally never used those folder for my documents/music/etc. It wasn't a problem until programs started putting their stuff in there. This is part of the "must-put-on-C:\" behavior you see in much win software that I loathe. A constant pain and reason that C:\ seems never to be big enough.
What I heard - this problem (removing files from folders like Documents, Downloads) happens only when you actually move storage of these. Yes, you can move Documents folder into D: and things will work just fine. But this is where this bug will hit you.
I moved my Downloads folder, nothing much to loose here, but I'll surely do a backup of everything before updating.