I can upgrade Graylog to 2.5 using the published method but what i will also need to upgrade the Elasticsearch to 6.x branch for 2.5.1.
No need to make the upgrade from ES 5 to ES6 in the same maintenance window. 2.5.x is supporting ES5 and ES6. Just do this one after another. First Graylog after that the Elasticsearch update.
Is there any published information on migrating existing data within Elasticsearch 5 to 6 for Graylog as a part of the upgrade from 2.4.6 to 2.5.1?
Please read the Release Notes of 2.5 ( https://www.graylog.org/post/announcing-graylog-v2-5 ) - we still miss the guide as some issues keep us busy not writing this guide - but if the check command did not return any indices, just read the ES upgrade notes and follow their upgrade guide.