What problems can I get if I delete Elasticsearch index directories manually instead of using the delete API?

My Elasticsearch cluster is out of memory. There are some indexes that can be dropped, but Sense queries are unresponsive, so I manually deleted one of those indexes and then tried to shutdown and restart all nodes in the cluster. This doesn't work, I get all sorts of errors. Is it dangerous to manually delete directories under / nodes / 0 / in order to get rid of the indexes?