As long as you cannot display it, I have no idea how to remove it.
AFAIK, a downtime which is set via command (instead of configuration = ruleset) is not part of the configuration and thus not found below the etc/check_mk/conf.d/wato/ directory, but is held in the state of the core (Nagios or CMC). Not sure how to act on that (or even check on it) if it’s not shown in the normal UI.
Something strange about the core’s state … I assume you have already restartet the site?