Usually is caused by a virus. the files are still there but the attribute of the files become hidden, so you can't see the files.
To see the hidden files you have to change the Folder Option View, in Windows 7
Open Windows Explorer (Right click On Start Button , then choose Open Windows Explorer)
On The Organize menu, choose Folder and search options
Click Apply and click OK
Now with this option (show hidden files,folders,and drives), the hidden file can be seen using Windows Explorer.
But the attribute is still in hidden. To change back to become normal attribute, you can use file attribute tools. So many tools on the internet, one is Febooti fileTweak you can download from its website http://www.febooti.com/
After downloaded and installed, go to file that you want to make change the attribute
Right click on File, then click properties
The Properties of the file will appear, and you can see the new tab named Attributes (from the febooti software), and then you can set and change the file attribute, Read only, Archive, Hidden, System, etc.
Click Apply or OK after make a change.
click on figure to enlarge