If you're processing payments via Braintree, and a transaction has for some reason not settled automatically (and is therefore only visible in your Braintree dashboard and not Piano), you shouldn't use the option in Braintree's dashboard to submit the transaction for settlement.
Because in case of settling the initiated payment manually in Braintree, the payment status itself won't be changed in Piano. So the user will be charged, but their transaction information won't be passed to Piano and the user won't gain any access.
If this charge has been manually authorized by you in your Braintree account, the expected behavior is that the access is not going to be updated and it won't show up as a completed transaction on Piano's end. The same behavior would be in case of a refund - if you would manually refund a transaction in Braintree, it will not be refunded in Piano.
In order to fix such an issue, you would need to refund this transaction directly in Braintree and ask the user to re-subscribe again.