Hmmm, maybe showing my ignorance, but why do you feel the need to use this function? Assuming you want to clean out excess "junk" audio clips before archiving a session, my method would be to remove all unused, followed by Save Session Copy(check the box to include audio files/clips) and send this copy to a drive that holds my archived projects. I would not use Compact, as I just hate to mess with the audio files(in case the compact function won't un-compress a few years from now). With storage space as cheap and plentiful, I would leave things as they are(though I would compress/zip for uploading to someone else).
If none of this addresses your concerns, maybe giving more detail on your end goal will get better advice
Last thing to remember re backups, if it doesn't exist in 3 places, its not backed up...