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

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