|change the attributes to show hidden, and make sure those folders are actually folders and not links. Many times a virus with hide your files and then produce fake copies of the origional, which link to a program the virus creator wants to be opened.|
fix for missing files(ussually)
open a command prompt and type in
(where %driveextension% is your drive letter...e,f,g)
then type attrib -h -s *.*
(then go back to your drive and see if your files reapear.)
to fix your actual issue, you will need to download a program like malwarebytes, or avast and have it scan the computer and the flash drive.