The "reload" function from console will remove the .lock file if your rtorrent is stuck and won't start on reboot.
Fail2ban IPs can be reset by restarting the service -- service fail2ban restart. You can also flush ALL rules from iptables with the command "sudo iptables -F" However if you have any other desired firewalls rules this will flush them as well.
What do you mean exactly suspend a seedbox? If you mean disable rtorrent then you could either kill rtorrent and disable the cron job (crontab -e) or temporarily comment out the startup line for rtorrent from the file /home/$user/.startup