Q. I'd like to tell my Linux iptables firewall to flush out the current configuration every 5 minutes. This will help when I'm testing a new rules and configuration options. Some time I find myself locked out of my own remote server. How do I reset Linux firewall automatically without issuing hard reboot?

A. You can easily flush out current configuration using iptables command and shell script combo. There is no built in option for this kind of settings. So you need to write a small shell script and call it from crontab file.

Create a firewall reset shell script

Create a /root/reset.fw script:

#!/bin/bash
# reset.fw - Reset firewall
# set x to 0 - No reset
# set x to 1 - Reset firewall
# ---------------------------------------------------------------------------------------------------------------
# Added support for IPV6 Firewall
# ---------------------------------------------------------------------------------------------------------------
# Written by Vivek Gite <vivek@nixcraft.com>
# ---------------------------------------------------------------------------------------------------------------
# You can copy / paste / redistribute this script under GPL version 2.0 or above
# =============================================================
x=1

# set to true if it is CentOS / RHEL / Fedora box
RHEL=false

### no need to edit below  ###
IPT=/sbin/iptables
IPT6=/sbin/ip6tables

if [ "$x" == "1" ];
then
if [ "$RHEL" == "true" ];
then
# reset firewall using redhat script
/etc/init.d/iptables stop
/etc/init.d/ip6tables stop
else
# for all other Linux distro use following rules to reset firewall
### reset ipv4 iptales ###
$IPT -F
$IPT -X
$IPT -Z
for table in $(</proc/net/ip_tables_names)
do
$IPT -t $table -F
$IPT -t $table -X
$IPT -t $table -Z
done
$IPT -P INPUT ACCEPT
$IPT -P OUTPUT ACCEPT
$IPT -P FORWARD ACCEPT
### reset ipv6 iptales ###
$IPT6 -F
$IPT6 -X
$IPT6 -Z
for table in $(</proc/net/ip6_tables_names)
do
$IPT6 -t $table -F
$IPT6 -t $table -X
$IPT6 -t $table -Z
done
$IPT6 -P INPUT ACCEPT
$IPT6 -P OUTPUT ACCEPT
$IPT6 -P FORWARD ACCEPT
fi
else
:
fi

Set permissions:
# chmod +x /root/reset.fw
Create cronjon to reset current configuration every 5 minutes, enter
# crontab -e
OR
# vi /etc/crontab
Append following settings:
*/5 * * * * root /root/reset.fw >/dev/null 2>&1
Please remember to set x to 0 once a working configuration has been created for your Linux system.

Test Iptables Script Remotely

How do I test iptables based script remotely over ssh session? How do I avoid lock outs?

iptables do not have pf like testing option. However, you can use a shell script and cron combo or just use the following syntax:
# /sbin/service iptables restart; sleep 20; /sbin/service iptables stop &
This way you can recover from bad syntax error. If you have your own script:
# /path/to/your.script.sh; sleep 20; /sbin/service iptables stop &
Above will allow you to test changes for a while and then turn off firewall completely. You will be able to login again using ssh after 20 seconds if locked out.

Source: http://www.cyberciti.biz/faq/linux-iptables-firewall-flushout-configuration-every-5minutes/