Hello,
You should have gone through 5.6 before upgrading to 6.0, at least for Kibana.
There is an upgrade assistant in 5.6 that will run the upgrade API for you on all indices and also mention the breaking changes between the versions.
You can still run it now, by connecting a 5.6 Kibana to your current 6.0 cluster and running the upgrade assistant for there, just to fix your watcher problem.
You can find the guide here and assistant is in the Management page of Kibana:
https://www.elastic.co/guide/en/kibana/6.0/xpack-upgrade-assistant.html