This seems like it should be easy to do, but, alas, it's not. I also cannot find any straight forward, step by step instructions on how to do this.

We had a customer who had multiple past due invoices (15+), by arrangement with us. Normally, we can give them the total of all and they can make a payment to one of the invoices, and by editing the amount of payment, get a credit on their account due to the overpayment. Then we can pay the other open invoices form the credit. For some reason, the client was prohibited from entering a payment larger than $200 per invoice payment. The client didn't want to pay 15+ invoices that way, so we sent a payment link equal to the balance due. This automatically becomes a sales receipt on their account for that amount. Client paid with a card at their business location.

Now the issue becomes how to apply the sales receipt money to the open invoices, as the sales receipt does not create a credit on the account, which one would think it should. The sales receipt payment has been deposited but can be reversed, if needed, as it hasn't bene reconciled.
Anything that seems like would be the correct option, doesn't exist or can't be found. HELP!