If a project is configured with a "blank" custom workspace in it's Advanced Project Options, then when the workspace is cleaned, $JENKINS_HOME is deleted.
More specifically, if the "Use custom workspace" option is ticked, but the "Directory" field is not filled in, then the workspace directory is effectively $JENKINS_HOME.
Presumably this is because (as the docs mention) the custom workspace is relative to $JENKINS_HOME.
This is a serious issue, because a workspace clean removes all Jenkins workspaces, all Jenkins job configuration etc. without warning.
Please protect silly people like me from myself!!!!!