When upgrading a cluster with a /_cluster/settings that disappears (or is changed and not properly registered by a plugin), then it becomes impossible to unset a persistent setting. Worse still, it then becomes a problem to apply new settings because it tries to merge the old settings.

PUT /_cluster/settings
{
  "persistent": {
    "unknown.setting": null
  }
}

should be allowed to run even though the setting is unrecognized.