Hi, I have a user that will have both VoiceMail notifications to email and VoiceMail alert to the actual handset. For some reason, even though the VoiceMail has been deleted from the email, the Voicemail indicator on the handset is still blinking. Is the email notification just an alert that not tied to the server?

Unless you have unified messaging for that user, the email is just a notification that contains a copy of the voicemail, and deleting it does not affect the actual voicemail on the server.