See http://www.helionet.org/index/topic/27636-solved-lets-encrypt-support-auto-ssl/ and http://www.helionet.org/index/topic/26914-ssh-on-tommy/?p=124952
In order to automatically renew Let's Encrypt a custom Heliohost plugin is going to need to be written which is a considerable undertaking, but it is in the works. For now just update your Let's Encrypt certificates manually.