So the problem is indeed that the cgroups are deleted using the
cgroupfs, and fuse doesn't get that information.  The fuse kernel module
is caching the information for one second before re-querying userspace.

I've pushed a patch to lxcfs to drop the caching to a half second.  I'm
posting a patch to lxc-devel to sleep for half a second during reboot.
This reliably fixes the race in my tests.

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https://bugs.launchpad.net/bugs/1514690

Title:
  rebooting container with systemd >= 226 fails to create /lxc/adt-
  xenial/init.scope control group

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