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
Actual Behaviour:
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.
Debug Token:
https://tricorder.pi-hole.net/Ijd0ga9X/
Fix
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.