If you’ve set this up to synchronise your users with Office 365 (or any other service which uses Azure AD on the back end) then you’ll have probably read the documentation I did which suggests re-running the setup wizard if you need to synchronise accounts outside the regular every-three-hours default schedule.
Thankfully there is an easier and faster way to do this.
Open PowerShell, and navigate to the install directory for the sync tool. This is probably C:\Program Files\Windows Azure Active Directory Sync. Run .\DirSyncConfigShell.psc1 and a new PowerShell window will open. In that windows run the Start-OnlineCoexistenceSync cmdlet, and your sync will begin.