This is one article in the larger Troubleshooting SharePoint Alerts guide
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.
- KB 936760 : The URL of alerts in e-mail notifications that you receive are incorrect after the URL of a … site in … SharePoint changes
stsadm -o updatealert -url http://yournewurl -oldurl http://yournewurl