Back up a (Flatpak-based) Gnome Boxes VM
Generally, the Gnome Boxes docs here should work when Flatpak is not involved. But when working with the Flatpak-based Gnome Boxes, the following steps must be used to back up a VM.
# enter the flatpak's sandboxed environment
flatpak run --command=bash org.gnome.Boxes
# list the gnome boxes domain names
virsh -c qemu:///session list --all
# dump the target vm's config to xml
virsh dumpxml $VM > $VM.xml
# locate the target vm's disk image
ls ~/.var/app/org.gnome.Boxes/data/gnome-boxes/images/
# copy both the config xml and the disk image to a backup location
cp $VM.xml /some/backup/path/
cp \
~/.var/app/org.gnome.Boxes/data/gnome-boxes/images/$VM \
/some/backup/path/