This article covers

There is no option to create a credit note for the payment-due invoices

Solution

Check the invoice whether a direct debit payment has been initiated against the invoice - and check the associated transaction is in in-progress status.

Direct debit payments are asynchronous payments- meaning, depending on the gateway, they take between 3-7 days to get settled.

At the end of this period, if the transaction is processed, an invoice will be marked as successful, and the invoice will be marked as Paid from Payment Due

Once the invoice gets marked as Paid, only then you would be able to initiate the refund/create a credit note- This is the expected behaviour with direct debit payments 

On the other hand, if it was a card payment, it would be marked as Paid immediately, and you would be able to issue the refund immediately.

Since the payment method is a direct debit payment method, you have to wait for the payment to be settled, before issuing a refund or before creating a credit note. Once a transaction is settled, create a credit note option would be available.

With the help of "The line items' billing period on the invoice" settings, the service period for the line items in the credit notes will be the same as their respective billing periods on the invoice.
Navigate to Settings > Configure Chargebee > Billing LogIQ > Billing & Invoices > Set default service period for credit note line items. Please refer to this link for more information.