From the terminal:
sudo rm /etc/pihole/adlists.list
pihole -g -f
Thanks, I have rebuilt the system. 
I would still like to highlight that even with default list blocks other internal lists from updating. Is there a way we can diagnose and fix this?
[i] Target: s3.amazonaws.com (simple_ad.txt)
[✗] Status: s3.amazonaws.com is blocked by https://adblock.mahakala.is. Using DNS on 8.26.56.26 to download https://s3.amazonaws.com/lists.disconnect.me/simple_ad.txt
[✗] Status: https://s3.amazonaws.com/lists.disconnect.me/simple_ad.txt (200000)
[✗] List download failed: using previously cached list
[i] Target: hosts-file.net (ad_servers.txt)
[✗] Status: hosts-file.net is blocked by https://adblock.mahakala.is. Using DNS on 8.26.56.26 to download https://hosts-file.net/ad_servers.txt
[✓] Status: No changes detected
[i] Target: hosts-file.net (grm.txt)
[✗] Status: hosts-file.net is blocked by https://adblock.mahakala.is. Using DNS on 8.26.56.26 to download https://hosts-file.net/grm.txt
[✓] Status: No changes detected
[i] Target: s3.amazonaws.com (simple_malvertising.txt)
[✗] Status: s3.amazonaws.com is blocked by https://adblock.mahakala.is. Using DNS on 8.26.56.26 to download https://s3.amazonaws.com/lists.disconnect.me/simple_malvertising.txt
[✗] Status: https://s3.amazonaws.com/lists.disconnect.me/simple_malvertising.txt (304000)
[✗] List download failed: using previously cached list
[i] Target: hosts-file.net (exp.txt)
[✗] Status: hosts-file.net is blocked by https://adblock.mahakala.is. Using DNS on 8.26.56.26 to download https://hosts-file.net/exp.txt
[✓] Status: No changes detected
[i] Target: hosts-file.net (emd.txt)
[✗] Status: hosts-file.net is blocked by https://adblock.mahakala.is. Using DNS on 8.26.56.26 to download https://hosts-file.net/emd.txt
[✓] Status: No changes detected
[i] Target: hosts-file.net (psh.txt)
[✗] Status: hosts-file.net is blocked by https://adblock.mahakala.is. Using DNS on 8.26.56.26 to download https://hosts-file.net/psh.txt
[✓] Status: No changes detected
How have you rebuilt the system?
https://adblock.mahakala.is is not one of the default block lists.
What is the output of:
cat /etc/pihole/adlists.list
wc -l /etc/pihole/gravity.list
Yes I rebuilt the system. I formatted the memory card, reinstalled Pi-Hole and went with default list.
I have carefully started adding new ones though. I am not sure which command to use to weed out incompatible entries so I kept doing:
tail -n20 /etc/pihole/gravity.list
sudo grep https: /etc/pihole/gravity.list | tail -n30
Both of which did not give any output. I considered this to be a good sign. I have added few custom list but only after posting the thread. At the time I ran my first update there were no custom lists added. After the first update, I started getting these errors (I always update via SSH). -- Ignoring the auto-update.
wc -l /etc/pihole/gravity.list
1 /etc/pihole/gravity.list
cat /etc/pihole/adlists.list
https://raw.githubusercontent.com/StevenBlack/hosts/master/hosts
https://mirror1.malwaredomains.com/files/justdomains
http://sysctl.org/cameleon/hosts
https://zeustracker.abuse.ch/blocklist.php?download=domainblocklist
https://s3.amazonaws.com/lists.disconnect.me/simple_ad.txt
https://hosts-file.net/ad_servers.txt
https://hosts-file.net/grm.txt
https://reddestdream.github.io/Projects/MinimalHosts/etc/MinimalHostsBlocker/minimalhosts
https://raw.githubusercontent.com/StevenBlack/hosts/master/data/KADhosts/hosts
https://raw.githubusercontent.com/StevenBlack/hosts/master/data/add.Spam/hosts
https://v.firebog.net/hosts/static/w3kbl.txt
https://v.firebog.net/hosts/BillStearns.txt
https://www.dshield.org/feeds/suspiciousdomains_Low.txt
https://www.dshield.org/feeds/suspiciousdomains_Medium.txt
https://www.dshield.org/feeds/suspiciousdomains_High.txt
https://www.joewein.net/dl/bl/dom-bl-base.txt
https://raw.githubusercontent.com/matomo-org/referrer-spam-blacklist/master/spammers.txt
https://hostsfile.org/Downloads/hosts.txt
https://someonewhocares.org/hosts/zero/hosts
https://raw.githubusercontent.com/Dawsey21/Lists/master/main-blacklist.txt
https://raw.githubusercontent.com/vokins/yhosts/master/hosts
http://winhelp2002.mvps.org/hosts.txt
https://hostsfile.mine.nu/hosts0.txt
https://v.firebog.net/hosts/Kowabit.txt
https://adblock.mahakala.is
https://adaway.org/hosts.txt
https://v.firebog.net/hosts/AdguardDNS.txt
https://raw.githubusercontent.com/anudeepND/blacklist/master/adservers.txt
https://v.firebog.net/hosts/Easylist.txt
https://pgl.yoyo.org/adservers/serverlist.php?hostformat=hosts;showintro=0
https://raw.githubusercontent.com/StevenBlack/hosts/master/data/UncheckyAds/hosts
https://www.squidblacklist.org/downloads/dg-ads.acl
https://v.firebog.net/hosts/Easyprivacy.txt
https://v.firebog.net/hosts/Prigent-Ads.txt
https://gitlab.com/quidsup/notrack-blocklists/raw/master/notrack-blocklist.txt
https://raw.githubusercontent.com/StevenBlack/hosts/master/data/add.2o7Net/hosts
https://raw.githubusercontent.com/crazy-max/WindowsSpyBlocker/master/data/hosts/spy.txt
https://raw.githubusercontent.com/Perflyst/PiHoleBlocklist/master/android-tracking.txt
https://raw.githubusercontent.com/Perflyst/PiHoleBlocklist/master/SmartTV.txt
https://v.firebog.net/hosts/Airelle-trc.txt
https://s3.amazonaws.com/lists.disconnect.me/simple_malvertising.txt
https://hosts-file.net/exp.txt
https://hosts-file.net/emd.txt
https://hosts-file.net/psh.txt
https://mirror.cedia.org.ec/malwaredomains/immortal_domains.txt
https://www.malwaredomainlist.com/hostslist/hosts.txt
https://bitbucket.org/ethanr/dns-blacklists/raw/8575c9f96e5b4a1308f2f12394abd86d0927a4a0/bad_lists/Mandiant_APT1_Report_Appendix_D.txt
https://v.firebog.net/hosts/Prigent-Malware.txt
https://v.firebog.net/hosts/Prigent-Phishing.txt
https://phishing.army/download/phishing_army_blocklist_extended.txt
https://gitlab.com/quidsup/notrack-blocklists/raw/master/notrack-malware.txt
https://ransomwaretracker.abuse.ch/downloads/RW_DOMBL.txt
https://ransomwaretracker.abuse.ch/downloads/CW_C2_DOMBL.txt
https://ransomwaretracker.abuse.ch/downloads/LY_C2_DOMBL.txt
https://ransomwaretracker.abuse.ch/downloads/TC_C2_DOMBL.txt
https://ransomwaretracker.abuse.ch/downloads/TL_C2_DOMBL.txt
https://v.firebog.net/hosts/Shalla-mal.txt
https://raw.githubusercontent.com/StevenBlack/hosts/master/data/add.Risk/hosts
https://www.squidblacklist.org/downloads/dg-malicious.acl
https://raw.githubusercontent.com/HorusTeknoloji/TR-PhishingList/master/url-lists.txt
https://v.firebog.net/hosts/Airelle-hrsk.txt
https://github.com/chadmayfield/pihole-blocklists/raw/master/lists/pi_blocklist_porn_all.list
https://raw.githubusercontent.com/chadmayfield/pihole-blocklists/master/lists/pi_blocklist_porn_top1m.list
https://zerodot1.gitlab.io/CoinBlockerLists/hosts
https://tspprs.com/dl/tracking
https://tspprs.com/dl/crypto
https://zerodot1.gitlab.io/CoinBlockerLists/list.txt
https://raw.githubusercontent.com/chadmayfield/my-pihole-blocklists/master/lists/pi_blocklist_porn_all.list
Sorry? I did not understand that?
What is the command to see if the list I've added (or all present) are being parsed properly and Pi-Hole is able to understand them.
This list that you have added (not one of the default lists) is known to contain a large number of false positives, including domains that serve other blocklists.
Note that despite this list blocking other lists, Pi-Hole has bypassed itself to download the requested list.
You are adding lists that won't block any more domains that you will ever run across, but will cause a large number of false positives and cause you trouble.
Just to quickly let you know, the reason download successded (pihole update) -- it is because I disabled Pi-Hole before moving ahead. 
Before I close this thread, is there a way I can verify which list are parsing correctly and which are causing issues to Pi-Hole's functioning?
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