It could simply be that they're marked "hidden" in which case you can simply go to
View > Hidden items (checkbox) in Windows Explorer.
If that's not it there could be file corruption on the hard drive. You can go to a command prompt and run
chkdsk x: /fwhere x: is the letter of the hard drive.
If that doesn't fix it you may have to try some file recovery software such as
EaseUSSteve