After upgrading to V12, z/OS jobs that end with the null terminator '//' will go into a state of ENDED_VANISHED and any activity performed in the TRAILER.MVS is not properly executed.
Internal handling of the // and logoff was changed in version 12, and this caused the logoff to not be handled correctly.
The issue was found and fixed with
Automation.Engine 12.0.8 in Agent MVS - released 5-6-2019
Automation.Engine 12.1.5 in Agent MVS - pending release
Automation.Engine 12.2.2 in Agent MVS - released 2-28-2019
Automation.Engine 12.3.0 in Agent MVS - pending release
Hotfix-Description: zOS Agent doesn't ignore logoff cards, job ends with status disappeared. A problem has been fixed where the zOS Agent does not ignore logoff cards in the JCL. The zOS Job ends with status disappeared.