From looking at the howto, it looks like your user list is going to be in /usr/bin/htpasswd. I doubt this directory will be backed up when you do a backup to desktop.
If I remember correctly, your templates-custom directories will be backed up.
So, do the backup to desktop and copy the /usr/bin/htpasswd file out to another pc so you can put it back when your upgrade is finished.
If you were doing an upgrade of the same box, I believe it would be ok, as is.
Hope that helps