Override.conf being deleted

I put this in /etc/systemd/system/apt-daily.timer.d/override.conf.

It speeds up the bootup time of my computer.

  [Timer]
  OnBootSec=15min
  OnUnitActiveSec=1d
  AccuracySec=1h
  RandomizedDelaySec=30min

However, something seems to be deleting this file as shown when I run

systemd-analyze

Bootup time goes from 42 seconds to 1.5 minutes.

How can I fix that ?

Can you post systemd-analyze blame | head -25

Ok, but I already restored override.conf

16.456s [email protected]
15.900s dev-sda1.device
14.647s systemd-journal-flush.service
11.892s keyboard-setup.service
10.085s systemd-modules-load.service
9.378s [email protected]
7.448s systemd-udevd.service
6.556s apt-daily-upgrade.service
5.377s snapd.service
3.689s NetworkManager-wait-online.service
3.210s NetworkManager.service
2.927s udisks2.service
2.692s networkd-dispatcher.service
2.671s thermald.service
2.650s systemd-tmpfiles-setup-dev.service
2.059s ModemManager.service
1.993s loadcpufreq.service
1.930s accounts-daemon.service
1.848s gpu-manager.service
1.724s apparmor.service
1.723s plymouth-start.service
1.481s plymouth-read-write.service
1.435s apt-daily.service
764ms wpa_supplicant.service
562ms upower.service

Would it be ok if I just copied override.conf back into the directory or do I have to use systemd?