From the FlexNet Manager Suite perspective, I'm guessing here that you have some kind of PowerShell script in place that connects to the Jamf API to extract data that is subsequently imported into FlexNet Manager Suite. To change how authentication to the API is done, you would likely need to make updates to that script.
In terms of what options for authenticating to the Jamf API are available, if you don't get responses here then you may find folk on the Jamf Community (Jamf Nation) have some insights.
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@cgresham - As FlexNet Manager does not have a productized inventory connector to JAMF, it is very likely that you have a custom solution that was created during your implementation of FlexNet Manager. This custom solution is normally created by creating a PowerShell Script that authenticates and connects to the JAMF API and the retrieved inventory data is then injected into FlexNet Manager via the Object Adapter Framework.
If you wish to modify how your JAMF Integration/PowerShell Script works, you will likely need to engage with the Team that created the script for you.
