Pete...The only files you'll need to copy from your reader to your computer are any books that you have on your reader. So, any files that have the extension ".epub, .pdf, .txt., .lrf,. lrx, .txt--I think that's all of them. You said in an earlier post in this thread that you only keep a few books on your reader, so this shouldn't be too hard to do.
Then after reformatting your reader, just copy the books you want on your reader back to the reader. You can do this with the Sony software, with Calibre, or with Windows Explorer.
It's actually a good idea to keep a backup copy of your books on your desktop anyway in case something happens to your reader. (The first time I ever reformatted my reader was because something on it got so corrupt that it was the only option I had.)
Hope this helps!
dordale