Pi-hole v6 is no longer storing its dnsmasq configuration details under /etc/dnsmasq.d/, to avoid conflicts with other tools writing to that directory.
But you can configure it to read that directory if you want to keep your custom configuration files, via misc.etc_dnsmasq_d.
Alternatively, if it is just one line, you can add that to misc.dnsmasq_lines under All settings » Miscellaneous.
All settings is available in Expert mode only.
See also Custom dnsmasq configs not loading.