[Test]
public void NHibernateService_UpdateA_SavesAWithSingleC()
{
    ClassA a = service.GetA(existingId);
    ClassC c = a.BArray[0].C;

    var newA = new ClassA
                   {
                       BArray = new[]
                                    {
                                        new ClassB { C = c }
                                    }
                   };


    service.UpdateA(newA);
}

[Test]
public void NHibernateService_UpdateA_SavesAWithIdenticalC()
{
    ClassA a = service.GetA(existingId);
    ClassC c = a.BArray[0].C;

    var newA = new ClassA
                   {
                       BArray = new[]
                                    {
                                        new ClassB { C = c },
                                        new ClassB { C = c },
                                    }
                   };


    service.UpdateA(newA);
}

NHibernate.NonUniqueObjectException was unhandled by user code
  Message="a different object with the same identifier value was already associated with the session: 162, of class: NHibernateService.ClassC

<?xml version="1.0" encoding="utf-8"?>
<hibernate-mapping xmlns="urn:nhibernate-mapping-2.2">
  <class name="NHibernateService.ClassA, NHibernateService" lazy="false" table="CLASS_A">
    <id name="Id" column="ID" unsaved-value="0">
      <generator class="native" />
    </id>
    <bag name="BArray" cascade="all" inverse="false">
      <key column="A_ID" />
      <one-to-many class="NHibernateService.ClassB, NHibernateService" />
    </bag>
  </class>
  <class name="NHibernateService.ClassB, NHibernateService" lazy="false" table="CLASS_B">
    <id name="Id" column="ID" unsaved-value="0">
      <generator class="native" />
    </id>
    <many-to-one name="C" class="NHibernateService.ClassC, NHibernateService" column="C_ID" not-null="true" cascade="all" lazy="false" />   
    <many-to-one name="Parent" class="NHibernateService.ClassA, NHibernateService" column="A_ID" not-null="true" cascade="all" lazy="false" />
  </class>
  <class name="NHibernateService.ClassC, NHibernateService" lazy="false" table="CLASS_C">
    <id name="Id" column="ID" unsaved-value="0">
      <generator class="native" />
    </id>
  </class>
</hibernate-mapping>

[DataContract]
[Serializable]
public class ClassA
{
    [DataMember]
    public int Id { get; set; }

    [DataMember]
    public IList<ClassB> BArray { get; set; }

    [OnDeserialized]
    private void GenerateBacklinks(StreamingContext context)
    {
        if (BArray != null)
        {
            foreach (ClassB b in BArray)
            {
                b.Parent = this;
            }
        }
    }
}
[DataContract]
[Serializable]
public class ClassB
{
    [DataMember]
    public int Id { get; set; }

    [DataMember]
    public ClassC C { get; set; }

    public ClassA Parent { get; set; }
}
[DataContract]
[Serializable]
public class ClassC
{
    [DataMember]
    public int Id { get; set; }
}

public int UpdateA(ClassA target)
{
    using (ISession session = GetSession())
    {
        session.SaveOrUpdate(target);
        session.Flush();
        session.Close();
    }

    return target.Id;
}

            var cs = new Dictionary<int, ClassC>();
            foreach (ClassB b in target.BArray)
            {
                // skip null or transient objects
                if (b.C != null && b.C.Id != 0)
                {
                    if (cs.ContainsKey(b.C.Id))
                    {
                        b.C = cs[b.C.Id];
                    }
                    else
                    {
                        cs.Add(b.C.Id, b.C);
                    }
                }
            }