After creating a new whonix-gateway and setting my whonix-workstation to use this newly created gateway as the NetVM I find that the various application config files don’t have their proxy settings updated.
I’ve identified that the script in /usr/lib/qubes-whonix/replace-ips exists and has the appropriate files included for updating, but they aren’t updated. Obviously the workaround is to manually set the settings but I’d be interested to know what’s going wrong.