I guess you can use Desktop -> System Settings -> Security Level and Firewall settings to first disable firewall. When you exit the program it should remove the existing /etc/iptables file. Then you can restart the Security Level and Firewall settings and activate the firewall. This should create a new /etc/iptables file when you exit the program. Though I am not sure if using Security Level and Firewall settings would interfere with the program you use.