tried to charge partial payment and then full amount but backspace

I now realize that there are plugins that could have handled this much better, but the service I provide necessitates a deposit at the start of the order and then the remainder to be paid when the order is complete. My attempt to make this work involved using a coupon code for the initial charge to get the price down to the deposit amount, and then after that deposit amount was paid, I changed the order status back to pending. When the order was complete, I used a different coupon code on the same order to subtract the original deposit amount so that only the remaining amount was left to pay. My customer said that they were able to charge the correct remainder amount to their card, but in Woocommerce I am only seeing the first payment, which was the deposit. In the order notes it does acknowledge a second charge at the completion of the order, but the transaction ID is the same as the first charge, and my transaction history only shows that first charge, not the 2nd one that the client did in fact pay. Where did the money go???