I am having a similar problem. Read the upgrade notice, glossed the cautionary notes, accepted the defaults and now my RPi3 Phiole Server is having DNS spasms rendering it unusable.
Running Bookworm on the server with all applicable updates.
Pihole is accessible for a few minutes and then it becomes "inaccessible" for DNS requests. The cycle repeats itself with regularity. It is the DHCP (sole) server in the LAN and that part is working fine per my limited knowledge.
Pi-hole diagnosis has one entry for an UDP packet (port 53 clue) to an IPv6 Address - Network unreachable. Understandable, since I don't use IPv6 in the LAN.
For DNS settings, I have:
Upstream DNS Servers: IPv4 Google
Pi-hole domain name: my domain name as recorded at name.com registration
Rate-limiting: 5000 queries within 60 seconds
Conditional forwarding: false,172.16.0.0/23,17216.0.2,domain.org
(the IP address range, pihole IP address & domain are correct - no fat fingering & prepared automatically during v6 upgrade)
Recommended setting: Allow only local requests - checked
Potentially dangerous options: all unchecked
Advanced DNS settings: all checked
There is a battery enabled RTC on-board with NTP sync service. The clock delta is presently zero (hope no DNSSEC issue).
Don't have the resources (image downloads, etc) to revert to v5 (yes, fully aware of the warning in the upgrade notice).
Would appreciate some diagnostic assistance, please. Thanks!
Had to purge the pihole-FTL database per @binderth to put Humpty Dumpty together again. Had never done that since the original installation several years ago and it had bloated to 9+ GB.