This is one article in the larger Troubleshooting SharePoint Alerts guide
Problem
When you setup an Alert in SharePoint the URL is stored in the content database as absolute URL’s and using the URL of the page you were using at the time (for example it could be intranet or intranet.yourdomain.com if using Alternate Access Mapping with external zones)
If you later change the url used to access your site (for example the name of the server, the host name, the port, protocol change from http to https etc) then the URL used in the email alerts will not change and may no longer work.
References
To Fix
Use STSADM’s updatealert command that was released in the SharePoint Administration Toolkit in April 2008 (see download links in above KB)
E.g.
stsadm -o updatealert -url http://yournewurl -oldurl http://yournewurl
