Thanks for the clarification. Before you wipe everything worth a read
here, about half-way down in the 'delete file' bit.
If you have not run it yet, run chkdsk - should be accessible via 'My Computer', rt click the drive, select 'properties'/'Tools'/'Check now' - and I would suggest running it with the 2 Check options unchecked first to see what you get. Then if you tick both options it should (hopefully) sort out any errors.