It appears that you may have set a different email template to be used when sending an estimate notification. Unfortunately, at this time I don’t see an option to change this in Method:New, so you will need to login to your account in classic in order to fix this. Once you are logged in, navigate to a transaction screen (e.g. Customers -> Estimates), select the More Actions… button and select Choose email template. If you have a custom template set for your Estimate Notification, simply clear the field and click Save & Close. This will set the template back to the default one. Once you have done this, the estimate notification email should now contain the link to portal URL.
Let me know if this works.