Reverting the commit Laney identified did resolve the issue for me.

(xenial-amd64)root@impulse:/home/bdmurray/tmp# dpkg -i 
ca-certificates_20180409ubuntu1_all.deb
(Reading database ... 34380 files and directories currently installed.)
Preparing to unpack ca-certificates_20180409ubuntu1_all.deb ...
Unpacking ca-certificates (20180409ubuntu1) over (20170717~16.04.1) ...
Setting up ca-certificates (20180409ubuntu1) ...
Updating certificates in /etc/ssl/certs...
WARNING: Skipping duplicate certificate Go_Daddy_Class_2_CA.pem
WARNING: Skipping duplicate certificate Go_Daddy_Class_2_CA.pem
8 added, 23 removed; done.
Processing triggers for ca-certificates (20180409ubuntu1) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.

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You received this bug notification because you are a member of Ubuntu
Touch seeded packages, which is subscribed to ca-certificates in Ubuntu.
https://bugs.launchpad.net/bugs/1764848

Title:
  Upgrade to ca-certificates to 20180409 causes ca-certificates.crt to
  be removed if duplicate certs found

Status in Ubuntu Single Sign On Client:
  New
Status in ca-certificates package in Ubuntu:
  Confirmed
Status in ca-certificates source package in Bionic:
  Confirmed
Status in ca-certificates package in Debian:
  New

Bug description:
  The certificate /usr/share/ca-
  certificates/mozilla/Go_Daddy_Class_2_CA.crt in package ca-
  certificates is conflicting with /etc/ssl/certs/UbuntuOne-
  Go_Daddy_Class_2_CA.pem from package python-ubuntu-sso-client.

  This results in the postinst trigger for ca-certificates to remove the
  /etc/ssl/certs/ca-certificates.crt file.  This happens because the
  postinst trigger runs update-ca-certificates --fresh.

  If I run update-ca-certificates without the --fresh flag, the conflict
  is a non-issue and the ca-certificates.crt file is restored.

  If I understand some of the postinst code correctly, --fresh should
  only be run if called directly or if upgrading from a ca-certificates
  version older than 2011.

  Running bionic with daily -updates channel and ran into this this
  morning due to the release of ca-certificates version 20180409.

To manage notifications about this bug go to:
https://bugs.launchpad.net/ubuntu-sso-client/+bug/1764848/+subscriptions

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