There is a possibility that your files have been deleted. So we have to check it first.
Go to "My Computer" for XP or just "Computer" in Windows 7/8. Right click the drive letter assigned to your flash disk or external hd. Choose Properties. Check the "Used Space". If it's not 0, then there are some files using it, even if you can't see it inside the flash disks window. We can then proceed on Unhiding/Showing it.
But first, we have to consider that your flash disk/external hd is infected by a virus. What we want to do is to get rid of the virus first. Update your Antivirus and Run a full scan. Why a full scan? Because since your flash disk/external hd is inserted to your computer, we can then assume that your computer is also infected. Then showing the files would be just for temporary because the virus will hide it again. So we have to remove the virus first.
If you don't have an antivirus installed in your system, i recommend using the free version of Malwarebytes.
After installing the product, you have to manually uncheck the first box that says "Enable Trial Version", we don't need that. We only need the free one. Update it, Run a Full system Scan including the flash disk/external hd.
We can now proceed on showing your files. Go to command prompt. (or Run then type cmd, enter). While on command prompt, type attrib -h -r -s /s /d G:\*.*. Replace the letter G depending on what your flash disk/external hd letter is assigned to. Ex. If it is F: on "My Computer"'s window, it would be attrib -h -r -s /s /d F:\*.*.
Then open your flash disk, You can now see your files.
Another way is to use the Folder Options. For XP, open your flash disk or external hd. Then Click Tools on the upper part of the window. Choose Folder Options > View Tab > Tick Show Hidden files and Folders and Uncheck Hide protected operating system files. You will be prompted with a warning, just choose Yes and Apply. You can now see your files.
For Windows 7/8, open your flash disk or external hd. Click Organize on the top-left corner of the window. Choose Folder Options > View Tab > Tick Show Hidden files and Folders and Uncheck Hide protected operating system files. You will be prompted with a warning, just choose Yes and Apply. You can now see your files.