Ticket 47729 - Directory Server crashes if shutdown during a replication initialization
    
    Bug Description:  When a shutdown was detected we marked that the total update was done
                      prematurely(prp->stopped).  This allowed the replication plugin to close
                      while the total update was still in progress. Other plugins continued to
                      be shutdown (e.g. ldbm database), while the total update was using shared
                      resources - which lead to a crash.
    
    Fix Description:  Only mark the total update protocol as stopped, after it is finished using
                      shared resources.
    
    https://fedorahosted.org/389/ticket/47729
    
    Reviewed by: nhosoi(Thanks!)
    (cherry picked from commit e7f7e9127717c1d432b10493b626fed334cc595f)