>From what I can tell, and according to my own tests, this is working
correctly. I think this is a misunderstanding of a couple things:

1. OnCalendar= can be specified multiple times, allowing multiple
trigger times. If you want to completely override the original setting,
you need:

[Timer]
# This empty entry clears the existing list.
OnCalendar=
OnCalendar=*-*-* 5:00

2. The original timer unit has RandomizedDelaySec=12h, which means the
time listed by systemctl list-timers may not reflect exactly what you
specify in OnCalendar=.

See
https://www.freedesktop.org/software/systemd/man/latest/systemd.timer.html
for more information.

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

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https://bugs.launchpad.net/bugs/2090941

Title:
  "systemctl edit apt-daily.timer" creates a file which is ignored by
  systemd timer

Status in systemd package in Ubuntu:
  Invalid

Bug description:
  On Ubuntu 24.04 LTS changing the apt-daily.timer with "systemctl edit
  apt-daily.timer" succesfully creates a file which is unfortunately
  ignored by systemd even after doing "systemctl daemon-reload" and
  "systemctl restart apt-daily.timer".

  To reproduce it try to change the timer of apt-daily.timer by calling
  "systemctl edit apt-daily.timer".

  Add the following lines:

  [Timer]
  OnCalendar=*-*-* 5:00

  Save and exit.

  Reload by calling:

  systemctl daemon-reload
  systemctl restart apt-daily.timer

  Now you can verify that the timer is not changed accordingly by
  calling:

  systemctl list-timers --all

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