Is there any chance that the people affected by this bug perhaps had an
upgrade policy such that the new config file shipped with openssh-server
would be taken as-is, instead of keeping the local changes?

If you changed the port, and then the upgrade was allowed to install the
new config file (because there were changes in the new config file
shipped in openssh-server), then the port would be restored to 22.

So when you guys experienced "connection refused", was that on the
custom port you had, and you didn't try port 22? Or was port 22 also
closed?

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https://bugs.launchpad.net/bugs/2087551

Title:
  OpenSSH server config broken on unattended update

Status in openssh package in Ubuntu:
  Incomplete

Bug description:
  My server performed unattended update of openssh-server from
  1:9.6p1-3ubuntu13.5 to 1:9.6p1-3ubuntu13.7, and after this I could not
  access ssh anymore, connection refused.

  Following the steps at the bottom of this post to use non-socket-
  based-activation has allowed me to connect to the server again:

  https://discourse.ubuntu.com/t/sshd-now-uses-socket-based-activation-
  ubuntu-22-10-and-later/30189

  I suspect this is related to using a non-default port, although the
  systemd socket configuration appeared to exist with correct values, as
  well as the custom port value in sshd_config, before making the above
  change.

  ProblemType: Bug
  DistroRelease: Ubuntu 24.04
  Package: openssh-server 1:9.6p1-3ubuntu13.7
  ProcVersionSignature: Ubuntu 6.8.0-48.48-generic 6.8.12
  Uname: Linux 6.8.0-48-generic x86_64
  ApportVersion: 2.28.1-0ubuntu3.1
  Architecture: amd64
  CasperMD5CheckResult: unknown
  CloudArchitecture: x86_64
  CloudBuildName: server
  CloudID: configdrive
  CloudName: configdrive
  CloudPlatform: configdrive
  CloudSerial: 20231014
  CloudSubPlatform: config-disk (/dev/vdb)
  Date: Fri Nov  8 13:13:51 2024
  ProcEnviron:
   LANG=C.UTF-8
   PATH=(custom, no user)
   SHELL=/bin/bash
   TERM=tmux-256color
  SourcePackage: openssh
  UpgradeStatus: Upgraded to noble on 2024-06-04 (157 days ago)

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