Apparently its because when you reset a master page to a site definition, MOSS somehow disconnects the copy file from the sharepoint server – consequently you cannot delete it and get the very annoying “This item cannot be deleted because it is still referenced by other pages”

There is a very easy workaround it seems – using sharepoint designer, create a new folder and move the culprit files into a new folder. Delete the folder and the files magically dissappear – no hiding, no frustration.

I’ve heard this also works for other MOSS file types locked in the same limbo hell.