Say we have a collection of course files, with an image among them. I put the image in a quiz. I then decide that I want to organize my course files into folders. Of course then when I go back to the quiz, the image is no longer displayed because the link is broken.

The best solution I could think of:
When images etc. are inserted in quizzes etc., a log is kept of the file which it is linked to. Then in the course file manager, when files are moved or deleted it checks against that log and warns the user that a link has been broken, and instructs them how to fix it (or automatically fixes it).

I know this is barely a bug, and perhaps more like a new feature. Sorry if my ticket typification peeves you.