Let’s Encrypt attempts to renew a certificate for a domain in Plesk, which has a CloudFlare certificate configured

Symptoms

The following notifications are received by Plesk Administrator:

The following domains have been secured without some of their Subject Alternative Names:
<none>
Could not renew Let's Encrypt certificates for example (login johndoe). Please log in to Plesk and renew the certificates listed below manually.
Renewal of the following Let's Encrypt certificates has failed:
<none>
The following Let's Encrypt certificates have been renewed without some of their Subject Alternative Names:
<none>

Cause

Expected behavior, when the following conditions met:

• The domain example.com has non-Let’s Encrypt Certificate public available (for example it has been configured in CloudFlare), or domain itself is hosted on another server but there is expired LE certificate assigned to the domain in Plesk in Domains > example.com > Hosting Settings > Certificate 
• Keep Secured configured in Subscriptions > example.com > Customize > Additional Services > Let’s Encrypt

In this case a certificate re-appears after running the task “keep-secured.php” in Tools & Settings > Scheduled Tasks.

Resolution

1. Log into Plesk as Admin.
2. Go to Subscriptions > example.com > Customize > Additional Services > Let’s Encrypt set to “None”
3. Go to Domains > example.com > Hosting Settings > Certificate and witch certificate to none.
4. Remove certificate in Domains > example.com > SSL/TLS Certificates.