When a user deletes a workflow package under /etc/workflow/packages that doesn't have replication privileges, it triggers a request for deletion workflow. That causes pages to get deleted from the publish instances.
Install AEM 6.2 cumulative fix pack 10 (available December 8th, 2017).
Install AEM 6.3 Cumulative Fix Pack 6.3.1.2 (available in the beginning January 2018).