When you raised the credit note did you choose to hold funds on account or refund them? If you chose to refund there and then, then it would have created a pre-tagged bank transaction at that point and you can just delete the untagged one (which is a duplicate).
If you chose to hold on account then you’ll have to find the relevant “payment” record (sales -> view payments -> advanced search -> set “type” to “unallocated”, then “submit search”), click through to the payment detail page and use the “refund balance” button at the top. Again, this will create a pre-tagged transaction on your bank account, then you delete the untagged duplicate.