See now this is different. The problem maybe simply permissions and how your nephew access/stored the files (assuming he isn't using a Linux/Android based computer). In Windows Explorer, click Tools>Options>View and make sure Show Hidden Files, Folders and Drives is selected, and uncheck (for now) Hide Protected Operating System Files. Click OK and then plug in the WD, can you now 'find' the missing files?
If this succeeds go back to the same View option and turn ON Hide Protected Operating System Files. If you do NOT, since VISTA numerous file changes were made and if you mess with them they cause Windows to corrupt and would require a reload. Many times they are just 'link' files to point to the 'new' location of where something used to be (for example a program looks for MY Documents, but now it is just called Documents, the link would be there for the program to point to the right location automatically).