Default iptables flushing

Due to the way I am setting up iptables I need to flush the default ones first, it appears doing so cuts net access to qubes connected to the first one, not unusual, the anomaly is that running iptables-save and inside qubes-firewall-user-script for testing purposes:

#!/bin/sh

iptables-save > /rw/config/iptables.savefile

iptables -F

iptables-restore < /rw/config/iptables.savefile

restores iptables to its original state BUT cuts off the internet access to other qubes, is there some kind of service I have to restart first?

For reference my end goal is the rearrangement of the default iptables since firewall.py would be a headache to configure to my pleasure.if it is a service that's the cause where exactly in this "script" should it be placed and which one is it?not qubes-iptables that's for sure

I haven't begun changing anything yet all I did was wiping and restoring, please do explain this anomaly to me.
Thank you