EDIT: I just hit the letsencrypt 5 certificate (per exact domain) per week limit.
Did you have an issue with generating _ecc certificate ?
Using your post the main website.com.cer file is being successfully generated, however the website.com_ecc.cer shows 0 bytes (the _ecc.key is fine).
But both certificates are issued by the same issue_cert method, so for some reason the main one works and the _ecc fails.