etc_dnsmasq_d Config not loading after updating to 6.1

At least not between v6.0 and v6.1, see the only change concerning dnsmasq config generation here. Actually, the last relevant change is > 1 year ago and was already part of Pi-hole v6.0:


When you specify a domain here, your Pi-hole generates a self-consistent configuration, taking into account everything it knows from pihole.toml (incl. conditional forwarding) but not from possibly existing external configuration (as you asked Pi-hole to manage this domain). If you do not want this local=// magic to happen, set dns.domain = "" (an empty string) to have Pi-hole stay away from assuming any configuration for you.

Have you tried this?