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.
AEM 6.0, 6.1, 6.2 and 6.3
This is a known product bug CQ-4221686.
The fix for this issue is only included in later AEM versions.
Install AEM 6.2 cumulative fix pack 10 (available December 8th, 2017).
Install AEM 6.3 Cumulative Fix Pack 18.104.22.168 (available in the beginning January 2018).