Quick Publish/WIP – needs work to make a bit more sense and explain things further.

If a profile is deleted from SharePoint, but is still in scope to be sync’d from Active Directory, unless a change happens in AD, FIM will not resync the profile to SharePoint in an incremental because it will assume the last sync from the metaverse is still present.  A delete from the Profiles list in SharePoint UPSA does not inform FIM, nor does FIM enquire when performing an incremental.

This is all coupled to how the Replicate Directory Changes permission allows FIM to request changes from AD.