You can update the external reference directly in the employee profile. However, if auto-assignment is enabled, the external reference cannot be edited until this feature is disabled.
Go to General Settings in the configuration (the cog icon in the top right-hand corner).
Head over to the Employee section.
Turn off "Automatically Assign Employee External References" and update the settings.
Go to the Employee that you need to update. You can update the External Reference in the Details Tab.
Click Update to save changes.
Once the External Reference is updated, turn the auto-assignment back.
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