Hi, I had a similar problem, and asked in this thread
yubiuser was very helpfull and gave me this answer:
Which version are you using? You can easily delete multiple or all blacklist entirety via Sql on the command line in version v5.
https://docs.pi-hole.net/database/gravity/
To delete all exact blacklist
sudo sqlite3 /etc/pihole/gravity.db "delete from domainlist where type=1;"