Hello Alshahim. The AttributeMetaData is the likely cause here. That entry still shows user="user name", which means the manager value was originally set through the identity creation form. Since the mapping was later changed to a Global Rule, the old metadata may still be preventing the new mapping from replacing or clearing that value. This is a known behavior when switching between direct mappings and rules.
As a test, remove just the <AttributeMetaData attribute="manager" .../> entry from one affected identity through Debug, then run an Identity Refresh with “Refresh identity attributes” selected. If that works, a controlled BeanShell task would be the way to handle it across multiple identities rather than editing them one by one.
Also confirm that the Global Rule is the only applicable mapping for manager. When the rule returns null, IIQ continues evaluating any remaining source mappings, so a later mapping could still provide a manager value.
Since manager is an Identity-type attribute, I would not return an empty string to clear it. Clear the stale metadata first and test the existing null return in a lower environment. Once the metadata is corrected and no later mapping supplies a value, the Global Rule should be able to clear the manager during identity refresh.