How to fix shortcut folders

If you did not format your flash drive, then check whether the
 files are not in hidden mode. 
Click on "Start" -->Run-->type cmd---> and click on OK. 
Here I assume your pendrive as G: 
Enter this command. 
attrib -h -r -s /s /d G:\*.* 
Note : Replace the letter G with your flash drive letter. 
Now check for your files in Pen Drive. 
You can delete the shortcut folders but don't get confused 
with the same filename from the original files.

derived from: Kioskea.net