You might want to try this as a quick and dirty workaround... First, I suggest you install Linux on a DIFFERENT flash drive, then boot your system and run Linux to examine the contents of your defective flash drive. This is MUCH easier than you might think, and you can do it without harming your existing Windows installation. Even better, you can use the same Linux flash drive to test any other flaky hardware in the future. Keep it handy and you will find yourself using it whenever something goes wrong. For example, if your optical burner stops working, boot into Linux and use the burner. If it doesn't work, the hardware is defective. If it works properly, you have a Windows (OS) problem or a software (APP) problem.
You can download a good (older, easy to use) version of Ubuntu Linux here:
http://old-releases.ubuntu.com/releases/10.04.3/ubuntu-10.04.4-desktop-i386.iso
it is a 700 MB file. Save it someplace easy to find it, maybe the Windows Desktop.
Next, you'll need an installer program to put Ubuntu on the flash drive. I recommend the YUMI installer, which works with the most popular Linux distributions here:
http://www.pendrivelinux.com/yumi-multiboot-usb-creator/
There is a link to the installer file on that page, along with a pictorial on how to use YUMI to install Linux on your flash drive.
Follow the pictorial to create the Linux flash drive, then boot your system with the Linux flash drive and use Linux to check the contents of the DEFECTIVE flash drive. If the missing files are visible under Linux, you can copy them to the Linux flash drive (IF space is available), to a different flash drive, to an external drive, or burn them to an optical disk (DVD if you have a lot of files).
Once you have safely copied the files and KNOW that they are not corrupted, you can reformat the defective flash drive under Windows to try to salvage it.
Good luck with this, please let us know what happens...
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