Lost/ruined RAW files
Have you tired putting the card back in the camera and seeing if you can view the files? I have had issues in the past when I could see files on the camera but couldn't copy them from the card. Normally I insert the SD card into my laptop and just use windows explorer to transfer the files, I managed to get around this problem by connecting the camera via a USB cable and copying the files across. If the images are missing the chances are the have been corupted in this case use a recovery program. Best place to start would be a google search for 'recovering deleted files from SD card', I have used undelete 360 which recovered files for me.