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The ArcGIS applications do not reflect changes to the license manager made from the Desktop Administrator.
The license manager change will not appear if you are also using an environment variable.
The ESRI_LICENSE_FILE and LM_LICENSE_FILE environment variables dictate the license manager used for all ArcGIS Desktop, ArcInfo Workstation and ArcSDE applications. This variable setting will override the license manager chosen during installation, and the license manager set in the Desktop Administrator.
If using the Desktop Administrator to manage licenses, remove the ESRI_LICENSE_FILE or LM_LICENSE_FILE envionment variable.
For help with setting a system environment variable, see: How To: Edit an environment variable.
Note: Direct Connect users can use the ESRI_ARCSDE_LICENSE_FILE variable instead of the ESRI_LICENSE_VARIABLE for the Direct Connect functionality.