Well I can't think of other commands to run to troubleshoot things as to the cause or what really happened. I was hoping someone else would jump in with ideas to run.
If you want to resolve the situation now, you can reboot the system. However, that will prevent additional troubleshooting steps, but I think to trigger it you might only have to run CA Backup.
If you do reboot now, comparing the earlier posted emHttp.txt file to one generated after the reboot and you verify the system is functional again might be interesting to see what exactly disappeared.