Hi, greenkeeperbistro. You can still process the super batch for all other employees first and leave this employee out for now. Their super liability will remain recorded, so nothing will be lost in the meantime.
In the meantime, you can request the employee’s stapled super fund through the ATO portal. If a stapled fund is returned, you can use those details. If not, you can then assign your default super fund. For more information, please see this article: Setting up Super Payments with Beam in QuickBooks Online.
Once you have the correct super details, simply update the employee’s profile and process their super in a separate batch. This approach will help you stay on track with your current pay run while remaining compliant with super requirements.
Please let me know if you need anything else. We're here to help.