I tested an upgrade from xenial to bionic today and did not receive a
conffile prompt regarding /etc/cron.daily/apt-compat and part of the
output you've pasted leads me to believe the file did not exist on the
system which you were upgrading. Have you run into this any more?

Additionally, I've sorted out the issue in ubuntu-release-upgrader for
Eoan. If you want it SRU'ed let us know.

** Changed in: apt (Ubuntu Eoan)
       Status: Confirmed => Incomplete

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https://bugs.launchpad.net/bugs/1796193

Title:
  unattended do-release-upgrade asks about /etc/cron.daily/apt-compat

Status in apt package in Ubuntu:
  Incomplete
Status in ubuntu-release-upgrader package in Ubuntu:
  In Progress
Status in apt source package in Eoan:
  Incomplete
Status in ubuntu-release-upgrader source package in Eoan:
  In Progress

Bug description:
  I'm trying to do some automated testing that involved upgrading a
  system from xenial to bionic, so I need it to not ask for user input.

  Before running do-release-upgrade, the system got a fresh dist-upgrade
  and reboot.

  To avoid interactive responses, I'm using:
  $ sudo do-release-upgrade -d -f DistUpgradeViewNonInteractive

  Part way through the upgrade, I do get prompted for something though:
  Preparing to unpack .../apt_1.6.3ubuntu0.1_amd64.deb ...

  Unpacking apt (1.6.3ubuntu0.1) over (1.2.27) ...

  Processing triggers for libc-bin (2.27-3ubuntu1) ...

  /sbin/ldconfig.real: Warning: ignoring configuration file that cannot
  be opened: /etc/ld.so.conf.d/x86_64-linux-gnu_EGL.conf: No such file
  or directory

  /sbin/ldconfig.real: Warning: ignoring configuration file that cannot
  be opened: /etc/ld.so.conf.d/x86_64-linux-gnu_GL.conf: No such file or
  directory

  Setting up apt (1.6.3ubuntu0.1) ...

  Installing new version of config file /etc/apt/apt.conf.d/01autoremove
  ...


  Configuration file '/etc/cron.daily/apt-compat'

   ==> Deleted (by you or by a script) since installation.

   ==> Package distributor has shipped an updated version.

     What would you like to do about it ?  Your options are:

      Y or I  : install the package maintainer's version

      N or O  : keep your currently-installed version

        D     : show the differences between the versions

        Z     : start a shell to examine the situation

   The default action is to keep your current version.

  Comparing the sha1 of apt-compat before the upgrade to another xenial
  system that has been unmodified, they are the same:

  In /var/log/dist-upgrade/main.log, I also found this:
  2018-10-04 14:20:24,575 WARNING got a conffile-prompt from dpkg for file: 
'/etc/cron.daily/apt-compat'
  2018-10-04 14:20:29,580 ERROR error 'a bytes-like object is required, not 
'str'' when trying to write to the conffile

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