@netn00b not sure if you found a good solution to this.
I do something similar with a script to update the IP's for my VPN in squid.conf
I've stripped my VPN config lines out into a seperate file (vpn.conf) and then replaced them with an include
include /usr/local/etc/squid/vpn.conf
This way the GUI is always correct and can be updated as normal and you can still keep your IP's current.