The fix is to seperate this 'upcoming shipment' into a 'club run' and 'normal' shipment. The 'old' 'upcoming_shipment' is changed and is used for club runs only. If a customer has a single slot membership used, this is considered a 'normal' email as the customer has already confirmed as the action required is a manual confirmation over the phone or via email. This would use the 'new' email template. The 'new' email templates - pickups and shipments - would run any time a winery hits 'create an order', 'create a shipment' or 'create' in the membership page.
Currently, we have an 'upcoming shipment' template, but this is used for template orders. If this 'upcoming shipment' is set to be enabled, this is sent for all non-club run orders (particularly manual shipment). The wording is confusing as the current communications page says 'membership shipment' instead of just 'shipment.'