The change we made today includes adding some new fields to the transaction_template XML including shipping_total and shipto_costs. The XSD file: http://admin.foxycart.com/v/0.7.2/xsd/transaction_template.xsd
These new fields are optional, so we don't think this change should have any negative impact on any systems using the XSD.
If you need to change your subscriptions and adjust the amount charged for flat rate shipping, you can do so by editing the subscription in the admin (or using the API). Whatever value a subscription is charging now will continue unless you modify them directly. If you previously adjusted the category to change flat rate shipping for your subscriptions, you'll now need to modify the subscriptions individually. Subscriptions that use live rate shipping will still use the amount configured in the admin for the categories involved in the subscription.
Please let us know if you have any questions about this change or if you run into any problems.