If the merchant or the customer has paid an incorrect subscription, instead of another service/product, then you can Remove the Payments from the paid invoice under Payments and Credits which will be added to Excess Payments. Then, you can transfer the excess payments to the Payment Due invoice by using the Apply Payments on the invoice.
Eg: For instance, a customer has Company A and Company B subscriptions/products/services/companies. The subscription Company A was incorrectly charged (from Checkout/Chargebee portal) instead of Company B on which the payments should be transferred from Company A to Company B.
Here is how!
Step 1: Open the incorrectly charged invoice from Subscription > Invoices> Incorrectly paid Invoice. Scroll down to 'Payments and Credits'' then click on the ellipsis button on the right-hand corner and choose 'Remove'.
You will get a notification that this amount will be added to excess payments. On clicking 'Confirm' this transaction amount will be moved to Excess payments.
Also the 'Paid' invoice will be moved to 'Not Paid' invoice.
You should also see the 'Excess Payments' under Customer Account.
Then you need to open the invoice that has to be paid which is in Payment Due and click on ellipsis button on the right-hand corner and choose 'Apply Payments'. The Apply Payments option will only be available if there are any excess payments.
Then, you will get a notification to choose the excess payment which will be starting as '#txn_…' and click 'Apply' by adding comments if any.
Then, the 'Payment Due' invoice will be updated as 'Paid'.
Now, you can see the difference between the invoices after these changes. Refer to the screenshot below.
You can also refer to this quick demo video from this link.