To re-enable them, you have to set misc.etc_dnsmasq_d to true either by editing /etc/pihole/pihole.toml or using the pihole-FTL command:
sudo pihole-FTL --config misc.etc_dnsmasq_d true
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Haha thank you, I hit this when I upgraded today.
Thank you for posting this. I hadn’t even noticed that my 99-second-DNS.conf changes were being ignored and I wasn’t getting two dns server assignments following my v6 upgrade.
