Both saying synced with AD however only one account exists
I’ve had to manually delete users from O365 during a DirSync deployment. Use PowerShell on the server running DirSync to run these commands:
Import-Module MSOnline
Connect-MsolService [Enter your Office 365 admin credentials when prompted]
remove-msoluser –userprincipalname UID@UPN.com
If the account is in Deleted Users in Office 365, append the last command with -RemoveFromRecyclebin
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