To restart your friendly neighborhood drupal bot when it no longer responds to commands, first kill the zombie bot for real.
When you kill it, the bot disappears from the channels so you don't have to kick it out, and the re-started bot will be able to claim its proper name.
On the server on which the bot module and bot_start.php is running:
ps -C "php bot_start" -opid | grep "[0-9]"
This gives you the pid, which you can use to kill the process.