If we make any changes to rc.netscaler and then reboot the appliance we do not see the changes retain. 

Even when the HA Sync and Prop are disabled NS will continue to perform the file sync from the primary to secondary by referencing the crontab file present in the /etc folder. 
If we want to make any changes to rc.netscaler, we need to hash out the nsfsyncd -p in the crontab so that secondary will not do a filesync from primary post reboot and that changes made earlier would be retained. 

Before change Crontab: 

SHELL=/bin/sh
PATH=/netscaler:/etc:/bin:/sbin:/usr/bin:/usr/sbin
HOME=/var/log
#minute hour    mday    month   wday    who     command
0       *       *       *       *       root    newsyslog
#
# time zone change adjustment for wall cmos clock,
# does nothing, if you have UTC cmos clock.
# See adjkerntz(8) for details.
1,31    0-5     *       *       *       root    adjkerntz -a
0        *       *       *       *       root    /netscaler/auto_update_signatures
*       *       *       *       *       root    nsfsyncd -p
35       0-23       *       *       *       root    nslog.sh dozip


After change Crontab:

SHELL=/bin/sh
PATH=/netscaler:/etc:/bin:/sbin:/usr/bin:/usr/sbin
HOME=/var/log
#minute hour    mday    month   wday    who     command
0       *       *       *       *       root    newsyslog
#
# time zone change adjustment for wall cmos clock,
# does nothing, if you have UTC cmos clock.
# See adjkerntz(8) for details.
1,31    0-5     *       *       *       root    adjkerntz -a
0        *       *       *       *       root    /netscaler/auto_update_signatures
#*       *       *       *       *       root    nsfsyncd -p
35       0-23       *       *       *       root    nslog.sh dozip

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Problem Cause

HA file sync was creating this problem.