You have to use drop in units or something in /etc, files in /lib are
not supposed to be modified.

** Changed in: apt (Ubuntu)
       Status: New => Invalid

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  update overwrites customized apt-daily.timer

Status in apt package in Ubuntu:

Bug description:
  Ubuntu 16.04.03 LTS
  apt (1.2.24)

  I customize /lib/systemd/system/apt-daily.timer on my public facing
  servers so they only update and reboot once a week, at an earlier time
  of day, to reduce downtime during a busy part of our day. The update
  this week overwrote the file with no notice or prompting that it was
  about to overwrite a customized file. This turned out badly as we had
  servers rebooting a couple days later at the worst time of the day.

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