Hi,
First a question, I'm confused about what you mean by "id". Is this the elasticsearch "_id" document id or some field you are setting exlicitely? In the first case, you can simply update the document without having to delete the old one, that should be done automatically.
Regarding the second part of your question: _delete_by_query gets a snapshot of the index when it starts and deletes what it finds using internal versioning. That means it is not concerned with marking or merging documents on the lucene shard level. That means, if the document changes between the time when the snapshot was taken and when the delete request is processed, you get a version conflict.