Automate Order Capture with Removed items

[Dualsided]

We have a delay in shipment that allows customers to contact us to change their order. This typically only involves removing items.

The problem we are running into is that when Shopify captures the order payment, it is capturing payment for the original authorized amount and not the new order total due reflecting the removed item(s). When editing an order, the Order JSON 'total_price' maintains and a new 'current_total_price' is created that reflects the new amount due (which is also displayed in the Admin as the 'Total due').

Example Use case:

1. Order Authorized for $100
2. $25 item removed before shipment. New Total due and 'current_total_price' is now $75
3. Order is captured for $100.
4. We now need to manually refund $25.

Has anyone run into this and have a solution on how to capture only the new order total due? Is a custom app the only solution?