What specifically are you seeing after you flush logs and it doesn't appear to work correctly? Which log(s) are you reviewing after you flush? Can you provide some examples if you have them available? Thanks.
On Admin Console > Settings clicking “Flush logs” whirrs away, then reverts to the default page.
Then going to “Dashboard” reveals that there are still the same “x” number of queries in the green box as before.
I might click “Flush logs” or “Disable query logging and flush logs” 3 or 4 times before I get an empty dashboard, and also occasionally SSHing to the Pihole to do “pihole -f”.
I have also found that since the new update end of last year/this year, I occasionally lose the gravity list. Dashboard will return a number that is only the same as the blacklist.
Updating gravity restores the “millions” of sites I usually have.
I’ve reinstalled PiHole on a smaller distro (Debian Stretch (arm64) by meveric) and reduced the number of block lists to 2, and everything seems OK for now.
I will return to this post if I have any further problems.