you did rm 95AddType00PHP2ibays.save, and it created a new file? Do you have some kind of wierd file-protection running? Try this:
# rm -rf /etc/e-smith/templates-custom/etc/httpd/conf/httpd.conf
...and then do this, as posted above:
If there are no files, do this, again at the shell prompt, and post the _exact_ output:
# /sbin/e-smith/expand-template /etc/httpd/conf/httpd.conf
# /etc/rc.d/init.d/httpd-e-smith restart
Note, "lost of conflicks" does not qualify as exact output.