Is there any procedure to link users to O365 apart from manual linking in SLM. There is only 50% of user linking to O365 connector.
Generally if users email id missing in ad account and user information not available in SLM then this problem coming and also make sure user/ad discovery enabled.
All users should be in same domain which is used to configure user account in o365 portal.
See blog post: What is user linking for Office-365 and how to manually link users in SLM
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