The purpose of Index Lifecycle Management is to automate that- you shouldn't need to manually delete documents. Like I said, you can do this from the Kibana UI by going to the "Edit template" UI. You can find it in:
Stack Management > Index Management > Index Templates > metricbeat-* > Edit > Page 3, Index settings
And then you can use the setting { "index.lifecycle.name": "93-Day-Retention-Policy" }