I found out that when you delete a record and upload the new Alert to another database, FNDLOAD does not automatically delete that record. So, to accomplish that i had to build in an extra funtion in the config file and add an extra parameter to the FNDLOAD command.
The extra parameter is UPLOAD_MODE='REPLACE'
and the additional function is
if :UPLOAD_MODE = 'REPLACE'
delete from alr_actions
where alert_id = (select alert_id from alr_alerts
where alert_name like :alert_name);
With this extra code, the records are first deleted and inserted by FNDLOAD....