(Excerpt from my internal KB)
[...] Each time there was a message "Error returning fulfillment (FID-999...) to license server (SERVER)", where "SERVER" refers to a machine that no longer exists. Afterwards the total license counts for all products on this LM were wrong. Some higher, others lower. Our corporate license admin (Ryan Gould) supplied a recipe that fully resolved the issue.
REPAIR CORRUPT LICENSE AUTHORIZATION
Delete the licensing trusted storage:
- After deauthorizing your Concurrent Use licenses, stop the ArcGIS License Manager Service and close ArcGIS License Server Administrator.
- In Windows File Explorer, navigate to the following directory: C:\ProgramData\FLEXnet
- Delete all ArcGIS related files from the FLEXNet folder (or if there are only ArcGIS related files, you can simply delete the FLEXNet folder).
- Return to the ArcGIS License Server Administrator and re-authorize your Concurrent Use licenses (including 3D Analyst).
- Verify the details in the Availability folder and in the diagnostic report from the License Manager. You might need to “Start/Stop License Server >> Re-read Licenses” to correct Availability.