Okay, since we are clarifying, Lightroom cannot write a raw file in the original camera format (i.e. NEF, CR2, RAF, etc.), and neither can Camera Raw. They are treated as read only files. You can delete them from the hard drive, but you cannot modify them. So when you export from Lightroom, if you want the raw image data then you have to export as DNG. Hence, a different filename and a separate file. If you do export JPEG images for a second time, and send them to the same folder, you have a couple of options. You can tell Lightroom to overwrite without asking or you can elect to save the file with a unique name.