After several weeks of intense testing, fixing configuration problems, re-indexing data and experiencing problems when upgrading our Kibana indices, we managed to upgrade our 36 Kibana instances and our Elasticsearch cluster in production from version 5.6.16 to 6.7.1 a couple of weeks ago.
We could not believe it but finally we had over 1.300 indices, 100TB of data, 102 000 000 000 documents and 18 Elasticsearch nodes running the last version of the elastic 6.x series at the moment.