Could you also post the exact command that you are using for the reindex? Feel free to black out the index name
Which version of Elasticsearch are you running? There have been a few bugs in the past
If you need a quick fix I would consider to expunge the deleted documents using the force merge API
https://www.elastic.co/guide/en/elasticsearch/reference/current/indices-forcemerge.html
POST /twitter/_forcemerge?only_expunge_deletes=true