It still seems strange that my original project file, with pointers to subdirectories, would be changed to point to where I backed up. I have one directory each for audio, images and narration (externally recorded). This structure is lost, understandability, during the backup.
It looks like the backed up SPJ file does not reference a directory for the media files. So my other option is to copy the backup directory as my new current project with everything in one directory.