Note that this can be done now with SQL commands. A few examples:
Remove all exact blacklist entries from the database:
sudo sqlite3 /etc/pihole/gravity.db "delete from domainlist where type=1"
Remove whitelist entries with a specific comment
sudo sqlite3 /etc/pihole/gravity.db "delete from domainlist where type=0 AND comment like '%source-2%';"
Remove blacklist entries for googlevideo
sudo sqlite3 /etc/pihole/gravity.db "delete from domainlist where type=1 AND domain like '%googlevideo%'"