This bug was fixed in the package update-notifier - 3.167

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update-notifier (3.167) xenial; urgency=medium

  * Use mktemp -p in the target directory to avoid a cross-filesystem move.
  * Also update motd if the dpkg status database has changed (LP: #1563854)

 -- Adam Conrad <[email protected]>  Mon, 04 Apr 2016 15:22:20 -0600

** Changed in: update-notifier (Ubuntu)
       Status: Confirmed => Fix Released

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https://bugs.launchpad.net/bugs/1563854

Title:
  update-notifier updates-available does not reset after dpkg run

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