The alert_cleanup.pl script will only clear out acknowledged alerts that are older than AMP Setup -> Historical Data Retention box -> Acknowledged Alerts setting. By default, the setting is 60 (days).

To run:
# scripts
(scripts is alias for 'cd /root/svn/mercury/scripts)
# ./alert_cleanup.pl
If you don't care about any of the existing alerts (acknowledged & unacknowledged), you can simply remove them all in a single command:
# dbc 'delete from alert;'
All deletes are final.