Não é possível extrair da matriz aninhada e consultar o subdocumento de retorno usando o MongoTemplate

// Query criteria for topic and reply
String topicId = "5e5e4d4bb431502946c15342";
String topicReplyId = "07a0293a-22a1-45fb-9aa2-775fa24e9915";

MongoOperations mongoTemplate = new MongoTemplate(MongoClients.create(), "test");
Query query = Query.query(Criteria
                               .where("topic._topicId").is(topicId)
                               .and("topic.reply._replyId").is(topicReplyId));
Update update = new Update().pull("topic.$.reply", new Document("_replyId", topicReplyId));
mongoTemplate.updateFirst(query, update, "topics"); // "topics" is the collection name

db.topics.aggregate( [
  { $unwind: "$topic" },
  { $match: { "topic._topicId": topicId } },
  { $unwind: "$topic.reply" },
  { $match: { "topic.reply._replyId": topicReplyId } },
  { $project: { _id: 0, reply: "$topic.reply" } }
] ).pretty()

{
        "reply" : {
                "_replyId" : "07a0293a-22a1-45fb-9aa2-775fa24e9915",
                "username" : "test1",
                "content" : "reply1",
                "date" : 1583240955561
        }
}