One of the things I did not like about the the split orders functionality in Super Orders v2.0 was HOW it split the payments and credits on an order. The code was written to move the product(s) selected to a new order and it simply copied over the original shipping, payments and credits to the new child order.
The ONLY way to correct this is to use the Edit Orders module and manually correct the child orders. That said there is a Super Order v1.3.9 upgrade fileset included with Edit Orders v3.0. If you are running Super Orders v2.0 (Rev 47 or 48) or v1.3.9, you can apply the patchs and you would be able to integrate Edit Orders v3.0 with Super Orders.
When we began the Super Order v3.0 work we decided to look at how to improve the split orders functionality. Upon really examining the split orders functionality, we realized that there was an order reconciliation issue. Orders could be split until there was nothing left to split, but there was NO WAY to reconcile the parent order to the resulting child orders. And for orders paid via PayPal or credit cards this was IMHO especially problematic. There was really no clean way to tie a group of orders to a single payment. Shopowners would have to manually keep track of this themselves outside of Zen Cart, and though they certainly could use the order notes to "tie" the orders together, there was nothing which explicitly linked the parent and child orders.
To resolve the order reconciliation issue, in v3.0 of Super Orders we opted to simplify the split order functionality. Instead of splitting orders to infinity and back we wanted to provide a better way to explicitly link a parent order to it's child order and clearly show the original payment data as well. So in v3.0 an order can only be split once creating a child and a parent order. The original shipping stays with the parent order, but the payment is divided between the child and the parent based on the remaining order balance in both (though now that you mention it we did not test how a GV would be split across the parent and child orders). We also clearly display the original FULL order amount on both the parent and child order along with the original FULL payment information. Additionally child orders where the original order was paid via PayPal, Authorize.net, or Linkpoint no longer erroneously display the PayPal, Authorize.net, or Linkpoint "Grey Box" notification area.
Now is there a way to keep the original ability to split an order multiple times, apply the correct shipping to each order, apply the payments, GVs, credit, taxes, and still provide a method to reconcile all the orders? Oh most definitely, but this would require a fair bit of work to execute a complete re-tooling of the split orders functionality.. AND when you're doing this work as a free contribution frankly it becomes a matter of who has bandwidth available to make all the necessary changes to support this.. So instead we opted for a simpler solution in order to solve most of the major problems we identified..
Hope this is helps you decide whether or not you decide to upgrade to Super Orders v3.0 or simply opt for adding Edit Orders v3.0 to your client's store and doing only the Super Orders v1.3.9 patch to support Edit Order integration.