It seems that the pihole stopped working, now it using the back-up DSN.
Your debug token is: afgq8gutxo
What specifically stopped working? I don't see anything major in your debug log.
It's not filtering anymore, I see the google ads for example. I think it reverts to the second (backup) DNS in my router settings.
Run a nslookup flurry.com on the device that's showing ads and the same command on the device that's running the Pi-hole.
What are the outputs?
Dnsmasq does complain about not finding some files, but according to the rest of the debug log they do exist?
May 16 10:53:27 dnsmasq[2760]: failed to load names from /etc/pihole/gravity.list: No such file or directory
The device that I am using is a Windows 10 PC.
On the Pi I see:
pi@raspberrypi:~ $ nslookup flurry.com
Server: 127.0.0.1
Address: 127.0.0.1#53
Name: flurry.com
Address: 192.168.1.232
What is the output on the Windows machine?
Server: FIOS_Quantum_Gateway.fios-router.home
Address: 192.168.1.1
Non-authoritative answer:
Name: flurry.com
Addresses: 74.6.136.153
98.136.103.26
212.82.100.153
I did try to repair the installation with -r and it seemed to work for for a while, then it started showing ads again.
Token: 5bkae7awll
Your router is set as your DNS on your windows machine (or at least a backup) and it responded to the DNS request.
Set-up only your pi address (192.168.1.232) as your sole DNS on your windows machine and test it again.
Well, yes, and in the router I have changed the DNS to point to the Pi. This is needed for all the devices in the house.
Hmm, let me restart the router.
Is that he only DNS there? Or do you have a backup DNS? Try leaving only the Pi-hole DNS.
I have rebooted the router and it works again. We'll see how long.
I have left one of the original DNS as the the back-up DNS in the router, for cases when the Pi would stop working, I am at work and my wife at home, calling me angrily 
Keep in mind that running a secondary DNS (as backup- non pi-hole) will most likely have queries processed by it and this, ad block will be sporadic.
Oh, really? I guess that's what is happening?
Because now again I see ads...
LE: Tried to set the same IP:
"Redundant DNS Entries: 'Primary' and 'Secondary' values may not point to the same DNS server."
Correct, you need a different DNS server ( a secondary device running pi-hole).
Shoot... Can it run on Windows ?
Are all the home routers this stupid?
Factory firmware on consumer devices is fairly limited.
There are several options out there depending on manufacturer model that would unlock the full potential of the device ...