Você pode usar o operador posicional para atualizar o documento incorporado correspondente.
Aqui está um exemplo dos testes (https://github.com/MongoEngine/mongoengine/blob/master/tests/test_queryset.py#L313)
def test_update_using_positional_operator(self):
"""Ensure that the list fields can be updated using the positional
operator."""
class Comment(EmbeddedDocument):
by = StringField()
votes = IntField()
class BlogPost(Document):
title = StringField()
comments = ListField(EmbeddedDocumentField(Comment))
BlogPost.drop_collection()
c1 = Comment(by="joe", votes=3)
c2 = Comment(by="jane", votes=7)
BlogPost(title="ABC", comments=[c1, c2]).save()
BlogPost.objects(comments__by="jane").update(inc__comments__S__votes=1)
post = BlogPost.objects.first()
self.assertEquals(post.comments[1].by, 'jane')
self.assertEquals(post.comments[1].votes, 8)
