Kind of Help / Kind of FYI (I found the fix for the issue)
We put our conditional forwarders in /etc/dnsmasq.d/02-name.conf
After updating to FTL v5.9, Web v5.6 and Core v5.4 conditional forwarders to some of the domains fail, reverse lookups and other domains work as expected.
The failing domains had parts with UPPERCASE. This wasn't an issue on past versions. Changing to all lowercase and a restart fixed the issue.