Wouldn't this change be causing the issue?
update-notifier (3.164) xenial; urgency=medium
...
* debian/99update-notifier:
- Now additionally triggers the an asynchronous background update of the
cached info via update-motd-updates-available hooking into
APT::Update::Post-Invoke-Success.
Here's the contents of 99update-notifier:
1 DPkg::Post-Invoke {"if [ -d /var/lib/update-notifier ]; then touch
/var/lib/update-notifier/dpkg-run-stamp; fi";};
2 APT::Update::Post-Invoke-Success
{"/usr/lib/update-notifier/update-motd-updates-available 2>/dev/null || true";};
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https://bugs.launchpad.net/bugs/1527710
Title:
apt-get update triggers asynchronous task
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