I, probably quite stupidly, decided to re-install es, but as a service. Which didn't work. reverted to the tar.gz distribution and now have different problems mentioned at: Elasticsearch red indices on upgrade
I have a mild theory that as all the indices were yellow the cluster couldn't form which in turn may have caused the watcher problem.
I reckon this may be because replicas were set to some number higher than was possible (considering the single node). I had more yellow indices after re-installing and setting number of replicas to 0 allowed them to turn green. But can't prove it would have solved the issue.