Found a nice article on serverfault.com describing how to easily remove a single rule iptables while it is running.

Use the --line-numbers option to iptables to get a listing which shows the line numbers for the rules in a chain e.g.

iptables -L fail2ban-SSH -v -n --line-numbers
Chain fail2ban-SSH (1 references)
num   pkts bytes target     prot opt in     out   source              destination
1       19  2332 DROP       all  --  *      *     193.87.172.171      0.0.0.0/0
2       16  1704 DROP       all  --  *      *     222.58.151.68       0.0.0.0/0
3       15   980 DROP       all  --  *      *     218.108.224.81      0.0.0.0/0
4        6   360 DROP       all  --  *      *     91.196.170.231      0.0.0.0/0
5     8504  581K RETURN     all  --  *      *     0.0.0.0/0           0.0.0.0/0

Then use iptables -D chain rulenum to remove the ones you don’t want e.g.

iptables -D fail2ban-SSH 1

would delete the

1       19  2332 DROP       all  --  *      *     193.87.172.171      0.0.0.0/0

line from the example above. Note that everything is renumbered so you can run the same command again to remove the new rule 1 in the chain.