Hi Elevationbook,
Thank you for your post.
In this matter, if the super payments have been processed twice, it is because they were authorized twice within the manage payment window. I would recommend speaking to the Super Fund for a refund. For the reconciliation, you would need to check the Pay liabilities window to see if the reverse transaction is sitting there. If yes, you'll need to reprocess the successful payments via the Pay liabilities window. For future reference and further information regarding this, please refer to this Help article: Reversing and Reprocessing Superannuation Payments.
Please let me know if you require any further assistance with this. I'm happy to help.
Cheers,
Princess