Hi,
Like Gonz said, there are some malwares that hide folder on your external drive. If you haven't tried yet, open my computer > Tools > Folder Options > click View Tab > under advanced settings, uncheck "Hide protected operating system files {Recommended}". and select "show hidden files and folders". Click Apply and then Ok to close the box.
In your external drive, you may see some hidden folders or drive with there icons fade out. Click on them, check to see if you can see the missing files?