Deletion of workflow package causes the nodes referenced by the package to be deleted from the publish instances
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.
AEM 6.0 and earlier versions
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 184.108.40.206 (available in the beginning January 2018).