Have you tried backing up the configuration and other files that you need instead of copying the whole root?
If you back them all up correctly, you should simply be able to restore the configuration, and there is no need to mirror the server.
Restoring is just a matter of
mkdir -p /tmp/backup/root
#Save packages installed
dpkg --get-selections > /tmp/backup/dpkg_packages
#Save nginx config
cp -R /etc/nginx/ /tmp/backup/root/etc/nginx
#Save installed repos
cp -R /etc/apt/sources.list.d /tmp/backup/root/etc/apt/sources.list.d
a) Copying sources.list.d back over
b) Re-adding pgp keys from sources and updating package list (apt-get update)
to reinstall all packages
dpkg --set-selections < /path/to/dpkg_packages
apt-get -u dselect-upgrade
d) Copying over the config