WAAD version 4.3.647.0 seems to have moved the powershell module for manual syncs. To put the shortcut back on the desktop of your WAAD Server. Simply create a new shortcut and paste in the details below and then type start-onlinecoexistencesync to perform a manual sync

powershell.exe -noexit -noprofile -file “C:\Program Files\Windows Azure Active Directory Sync\DirSync\ImportModules.ps1”