You could try creating a simple action that just invokes the Save As command and run it using the Batch feature of the CS File Browser. If you want to make duplicate files, it seems that it would be easiest just to back up all your NEFs before you start working on them, which is certainly a good idea in any event. Beyond a normal back up like that, I'm not sure what further protection you are looking for. When you use ACR to convert a NEF or other RAW file, it leaves the NEF file unaltered and saves the RAW conversion settings in a separate sidecar file (XMP file). The converted file that is opened for editing in Photoshop will be saved in one of Photoshop's usual formats (usually psd, tif or jpg)--you can't save it as a NEF. So, if you do a back up before you start working, then you will always have two copies of your NEFs.
BTW, if you upgrade to CS2, Bridge replaces the File Browser and will easily let you duplicate any file you select.
