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In System Center Configuration Manager, when you set the Site Code of a Software Metering rule to a secondary site, that rule will not be applicable to any clients.
This is expected behavior.
SMS 2003 Advanced Clients and Configuration Manager clients within a secondary site boundary also obtain policy from the primary site’s site database. If the Site Code of a Software Metering rule is set to a secondary site, no policy will be generated for that rule, so that no clients will receive that rule. You must set the “Site Code” of a rule to a primary site’s site code to make it assigned to clients.
(http://go.microsoft.com/fwlink/?LinkId=151500)for other considerations.
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