The file /etc/rc.d/init.d/xntpd is not listed as a configuration file in xntp3-5.93-14.i386.rpm. Almost all other RPMs list files in this directory as configuration files. The consequence of this is that any local changes get wiped out when upgrading the package.
xntpd has been replaced by ntp, file /etc/rc.d/init.d/ntpd is marked as %config.