This is what we have done BUT we have also had issues with this.
When we delete the registrants associated with an event, there always seem to be a number of registrants who are NOT deleted and are not visible in the back-end but are still associated with the event.
On the event landing page, there are still 37 registrants listed in relation to the event. Clicking on the number 37 in the Events Manager, leads to the Registrants Manager page for that event - which is empty.
If I then view the database in phpmyadmin and run an sql query based on the event id, the "left over" registrants show up.