I recently found this out myself through trial and error.  Doing this restores the default system files, but you don't have that ugly "icon not found" image anymore.

What you need: An icon theme you know has all icon types. (or at least all the Windows ones)

First, apply the custom icon theme.  Then, simply apply the Windows default one.  This should fix most icon problems you have.

When I did this, I used the "Quest" icon theme (from the Quest suite) as the intermediate step.  Applying the default icon scheme fixed my broken icons.

NOTE: You *might* have to reset custom icons you had for some files.  I hadn't messed with those too much so I don't know.

edit: I didn't take any screenshots, and don't feel like purposefully messing up my icons in order to illustrate this...

Never mind, still having issues.  I'm on technet trying to sort it out... as soon as I figure it out I'll post it here.