Workflow package deletion kicks off request_for_deletion workflow on the contents of the package instead of the package itself. It causes the unexpected deactivation of the pages from the site.

Environment

AEM 6.1 SP2.

Resolution

1. Go to http://hostname:port/system/console/configMgr.
2. Search Page Manager Factory.
3. Set the Page Subtree Activation Check property to true.
4. Click Save.