We have encounter this issue.
While setting up AD FS and enabling Single Sign-On into Office 365 and SharePoint online the following scenario caused some decent pain:
After the pretty straightforward installation and successful first synchronization the customer reported that one person is missing within the available active users inside of the o365 portal. Against all expectations
we didn’t face any of the obvious and well documented symptoms.
Work around:
https://www.techtask.com/one-or-more-on-premise-ad-objects-dont-sync-to-office-365-aad/?doing_wp_cron=1547771934.3955740928649902343750
Hope this helps!
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