Your assessment on cloning and export are correct. Reactivation as a result of cloning might be sidestepped with suitable usage of some vboxmanage commands on the clone (which would have to be researched, I don't know them right off).
Backup is a complete copy of the guest folder and all files & folders therein, as well as any guest disks that have been manually placed outside the guest folder. The guest should be completely shut down from within the guest OS if possible.
You can't use a backup copy of the guest folder and the original guest folder at the same time, no. UUID's would be the same, and Virtualbox would cry foul.
To restore a backup you simply copy the backup guest folder over the top of the existing bad guest folder. All Virtualbox processes should be off, not running, preferably after a host reboot. Removing/Adding should not be necessary. If you're absolutely sure that you don't need anything in the bad guest folder, you can delete it before copying the backup. You can also change the bad guest folder's name, which completely hides it from Virtualbox.
Rarely, due to host glitches (or Virtualbox glitches) a delete-snapshot process fails and might leave the guest in a dead state. Thus the need for a complete backup of the original guest.