Here are some hints to use at the command line.

$QMAILDIR presents the qmail home directory, often  /var/qmail  or  /var/local/eqmail .

Q: How can I remove all messages from the queue?
A: Stop eQmail:  qmail-send  AND  qmail-smtpd . Make sure that  qmail-inject  and  sendmail  can not be invoked. Easiest way is to do a  chmod -x  . Make sure that no other (cron) job will invoke them by bypassing the x-bit. Then run:

find $QMAILDIR/queue/*/*/* | xargs rm -f

Undo the preparations and start eQmail.