alter/remove specific popup notifications
You are in the right path, if you look at the CRM_Core_Session class you'll see the method getStatus which takes a boolean as a parameter, if TRUEthen it will reset the status.

That said, I would create a extension or use an existing one and implement hook_civicrm_postProcess. 

You'll need to know what is the class/form name of the form you are targeting, an easy way would be to inspect the source of the form/page from which you want to remove/replace the notification and search for .tpl 

Example: CRM/Contact/Form/Task/Email.tpl, its class/form name would be  CRM_Contact_Form_Task_Email

Then in your extension:

function myextension_civicrm_postProcess( $formName, &amp;$form ) {
    if($formName == 'CRM_Contact_Form_Task_Email') {
        $session = CRM_Core_Session::singleton();
        // Reomve status message from form
        $session-&gt;getStatus( $reset = TRUE );
        // Set your new message
        $session::setStatus(ts('This is a custom message.'), ts('Custom Message'), 'success');
    }
}