Running it with --simulate we can see something weird is going on:

sudo APT_CLONE_DEBUG_RESOLVER=1 apt-clone restore-new-distro 
/tmp/apt-clone-state-ubuntu.tar.gz bionic --destination / --simulate
missing: 
adwaita-icon-theme-full,fonts-cantarell,fonts-nanum,fonts-takao-pgothic,gir1.2-totem-plparser-1.0,gnome-session,gnome-themes-standard,gnome-themes-standard-data,gnome-user-share,gpart,gtk2-engines-pixbuf,ipython3,kerneloops-applet,libboost-date-time1.62.0,libboost-filesystem1.62.0,libboost-iostreams1.62.0,libboost-system1.62.0,libboost-thread1.62.0,libcanberra-gtk-module,libcanberra-gtk0,libcapnp-0.5.3,libcdio-cdda1,libcdio-paranoia1,libcdio13,libdfu1,libfreerdp-cache1.1,libfreerdp-client1.1,libfreerdp-codec1.1,libfreerdp-common1.1.0,libfreerdp-core1.1,libfreerdp-crypto1.1,libfreerdp-gdi1.1,libfreerdp-locale1.1,libfreerdp-plugins-standard,libfreerdp-primitives1.1,libfreerdp-utils1.1,libfwupd1,libgom-1.0-common,libicu57,liblouis12,libntfs-3g872,libpython-stdlib,libwinpr-crt0.1,libwinpr-dsparse0.1,libwinpr-environment0.1,libwinpr-file0.1,libwinpr-handle0.1,libwinpr-heap0.1,libwinpr-input0.1,libwinpr-interlocked0.1,libwinpr-library0.1,libwinpr-path0.1,libwinpr-
pool0.1,libwinpr-registry0.1,libwinpr-rpc0.1,libwinpr-sspi0.1,libwinpr-synch0.1,libwinpr-sysinfo0.1,libwinpr-thread0.1,libwinpr-utils0.1,linux-headers-4.13.0-16,linux-headers-4.13.0-16-generic,linux-headers-4.13.0-21,linux-headers-4.13.0-21-generic,linux-headers-4.13.0-38,linux-headers-4.13.0-38-generic,linux-image-4.13.0-16-generic,linux-image-4.13.0-21-generic,linux-image-4.13.0-38-generic,linux-image-extra-4.13.0-16-generic,linux-image-extra-4.13.0-21-generic,linux-image-extra-4.13.0-38-generic,python,python-minimal,python-pexpect,python-ptyprocess,python2.7,python2.7-minimal,python3-decorator,python3-ipdb,python3-ipython,python3-ipython-genutils,python3-pickleshare,python3-prompt-toolkit,python3-pygments,python3-simplegeneric,python3-traitlets,python3-wcwidth,tcpd,ubuntu-gnome-desktop

Some of those packages are in main. I was able to workaround this by
setting "allow-insecure=true" in the sources.list file in the apt-clone
file, but that is not a solution.

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https://bugs.launchpad.net/bugs/1756862

Title:
  upgrade from 17.10 to 18.04 - apt-clone crashed with SystemError in
  commit(): installArchives() failed

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