If the transactions are still appearing within the BACS Export screen, then this indicate that the Save button was not pressed when marking the transactions as successfully exported.
To resolve this, you can do the following:
Navigate to Creditors, Transactions, BACS Export
Select all of the transactions that are still appearing and press Process
Re-enter the Payment Reference and Date
Press the Export button
In the confirmation screen, press the Save button
The new exported file can be deleted as this will not be needed.