This situation does come up where a customer pays for an invoice but had forgotten to apply the discount. You would like to account for the discount however there's not a way to retroactively apply it. What happens is once the invoice is completely paid for and discount is needed to be applied, you would need to create an overpayment invoice. Here's a support article on how to do so:
Let's go over two examples illustrating how we can perform this action.
Creating an Adjustment
The first method and most recommended one would be to create an adjustment on the specific item that they had overpaid on. In this case, this is a class with two fees on it. I'll go ahead and select to "Edit Invoice":
From here, I'll need to select which fee I want to show as having been overpaid in order for the discount to apply towards it. Let's go ahead and select the "Registration Fee". A pop up window will display showing the fee as fully paid off:
For this case, the customer should have applied a $10 discount which they had forgotten to do. So I'll be setting the price of the fee of the amount that it should be before the discount:
Once I've selected to Save Changes, an adjustment up on the original fee will display and the status of the invoice will reset to PARTIAL:
From here, you'll just need to apply the discount you were originally intending to apply. I've went ahead and done that:
Now the invoice denotes the customer having overpaid as well as showing the discount now having been applied. From here, you can issue any refunds or credits towards the amount they had overpaid.
Adding a Fee
Here we have a fully paid invoice but the student had forgotten to apply the discount. Since the student had overpaid on the invoice, we would need to treat this as an overpayment. First, let's added a fee to the invoice:
In the notes, I'm referencing the discount that was missed leading to the overpayment. The discount was supposed to be for $10.
After adding the fee, we need to re-allocate the payment to point towards the fee. This allows us to refund that remaining amount. If you're not too familiar with payment allocations, here is a support article that discusses this:
Once you're on the payment allocation, you would need to select on the drop down where the payment originated from. In this scenario, I only have one payment. Notice that the payment is only applying to the class fees and not to the overpayment fee:
I'll need to allocate $10 of the original payment to the overpayment fee in order to refund it. Let's go ahead and add that while adjust the other allocations lower:
After I've updated the allocations, I'll go back to the invoice and add the discount. Note that the discount amount is for the amount of the overpayment fee:
Once added, the discount will apply to the class (as long as the class is eligible for the discount), and I can go ahead and refund the student the $10 they had overpaid:
If you're not sure how to process a refund, review this support article here: