Seems that as time goes by, every time we update its gonna mean a) we drop all existing contacts and preferences and start over from scratch, or b) we have do to careful manual editing and such to upgrade.
Idea:
Have an update script that you run before you update. It will store all your users personal info in a separate file. Update your installation, then run the update script again and it restores those preferences, appropriately modified to fit any changes.
I might work on this once I've finished my automated install script