Hi Jeff,
The Host Client VIB does not provide endpoint.cfg, that file is there on the base system.
Modifying the file should result in your changes being saved after a reboot, it is strange that this is not happening. I do wonder if the backup script did not have a chance to run. Can you try making the modification again, waiting 15 minutes, then rebooting the machine? Please also post the output of
ls -la /etc/vmware/rhttpproxy
so I can check the permissions and attributes of the file.
Also, what version of ESXi are you using and was it upgraded from an older version?