Thanks for the response. I haven't been able to identify the root cause leading to the missing file. Elasticsearch has been running on a server without me doing anything.
The cluster only has one node but I have a snapshot from a few days back. What's the recommended procedure to "wipe this node"? Unistall Elasticsearch, remove /var/lib/elasticsearch, reinstall Elasticsearch and then restore from snapshot? (I'm running Debian and using apt-get to install ES if it matters.)