collection.cs

foreach (var child in source.ChildCollection)
{ 
  var targetChild = target.ChildCollection.SingleOrDefault(c => c.Equals(child)); //overwrite Equals or replace comparison with an Id comparison
  if (targetChild == null) 
    target.ChildCollection.Add(Mapper.Map<SourceChildType, TargetChildType>(child)); 
  else 
    Mapper.Map(child, targetChild); 
}