If you un-check the box in the configuration wizard to prevent the initial synchronization from happening, you can fire the initial synchronization using DirectorySyncClientCMD.Exe.
How to force full sync if required
Run the following :
If AADsync is using OU filtering and OUs are added or removed, is an initial or delta synchronization required? In DirSync, changes such as OUs would required a full import/full sync.
Would love to know why the initial switch only appears to work once and then afterwards only runs a delta even when the parameter is specified. Any time a change is made to OU selection or scope filters a full sync is necessary.
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