Apologies for any confusion. What I mean is, if the invoice has previously been tagged as paid, then there’s likely to be a duplicate bank transaction, and a duplicate for the credit note too.
If the invoice was never tagged as paid (e.g. because the payment hadn’t cleared), the credit note would have cancelled out the value of the invoice so there is technically nothing to tag. In which case, you can delete the bank transactions - they cancel each other out and as far as everything else is concerned, the invoice has been settled.
Providing everything else balances - your bank account is correct, your money owed is correct - then deleting the transactions should be fine.