I have a similar situation, although I don’t use the WordPress Database Backup plugin. All entries disappeared at once at our customer’s web site. Unfortunately I can’t send more info from our customer, because he can’t tell us any details.
But here’s some info from our side: The table wp_em_events was completely empty, so I’ve restored some entries manually from a previous backup. Then I’ve recovered the corresponding entries from the wp_posts table according to the post_id field. So now I see those events using the [events_list] shortcode, but the events list (wp-admin/edit.php?post_type=event) is still empty.
Something still seems to be missing, what could it be?
(Thanks for this great plugin.)