Something very like that happened to my Seagate Free Agent 320 GB external hard drive. I had just copied over a huge multimedia collection, lots of folders full of music videos, films, mp3 collections, and the next time I went to check them out, I had lots of folders and sub folders, but they were all completely empty!
Suppressing the urge to (a) scream out loud (I had, in a rash moment, moved rather than copied the folders), and (b) start fiddling around with disk tools -- I did a bit of Googling and (1) used the "safely remove hardware" icon in the taskbar to stop the drive (2) completely powered down the computer and removed the plug from the wall (3) unplugged the USB cable and plugged it into another USB socket (4) powered back up again. Everything was as it should be.
If you right click the drive in Explorer, choose Properties from the menu, click the Hardware tab, highlight the correct disk drive, click the Properties button, choose the Policies tab, you can see if the drive is optimised for performance or quick removal.
Performance implies write caching which can result in a corrupted filesystem if you unplug the drive (or there is a power failure) when there are pending writes that need flushing from the buffer (This is what the safe removal icon does).
Quick removal implies always writing everything to the drive immediately which can slow down performance of the whole system, but means you don't have to use the icon, and (in theory) you are less likely to suffer filesystem damage. Choose the one you feel happiest with - you can always change it if you don't like it.
