Login on your shell, type ps -x to see what process number the bot has.
write kill pid (the process number)
when the bot is "dead" write rm botnick.user (whatever name you set for your userfile) also rm botnick.chan to get rid of the channel list.
once this is done do a ./eggdrop -m botnick.conf again and the bot will be restarted with no user record.