Helper scan fails over 90000 documents?
Is is not really clear if you set the size of the scroll to 900000 or bigger or if you are just looping over more documents by keep calling the scroll. What could happen is that handling the data takes to much time before you return to the scroll. The context is kept a default amount of time that you can configure using the scroll parameter as described in the following url:
https://www.elastic.co/guide/en/elasticsearch/reference/current/search-request-scroll.html