Every 2 minutes 0.debian.pool.ntp.org queries by both Raspberry Pi's in my network

[deHakkelaar]

@tomislief

First, why I am starting to have this issue when I enable IPv6? All was good when I was using IPv4.

It might have to do with the IPv6 GUA prefix changing by your ISP upstream which comes from your router via "router advertisement" or short RA:

IPv6 | Global addressing

Which in turn triggers a series of events which does not happen with IPv4.
Below posting hints to RA ... and the thread is full of related info:

WARNING: Raspbian October 2021 release bullseye + unbound

It's only an issue if openresolv is installed instead of classic/slim resolvconf, and it caused other issues already like restarting Unbound every time an RA with changed info is received. Basically it doesn't seem to work well at all with setups where a local resolver is meant to be used by the network instead of by the local host only. So instead of working around all the issues that openresolv causes, what about replacing it with resolvconf when installed as part of the Pi-hole installer?

EDIT:

@tomislief

Second, why does my other raspberry pi (cups printerserver) in my network still have the issue? It has no unbound installed. Is there anything that I can do about this?

Have you tried a good old trusty reboot?