AutoSSL doesn't renew certificates it did not issue

Symptoms

You may receive the following warning from the AutoSSL system when it fails to renew a certificate:

The certificate will not renew via AutoSSL because it was not issued via
AutoSSL to exampledomain.com

Description 

This is the default behavior for AutoSSL, as we do not want the AutoSSL system to potentially overwrite a higher-level certificate, such as an EV or OV, with a DV certificate. However, this behavior can be overridden.

Workaround

1. Log in to WHM as the ‘root’ user.
2. Navigate to "Home / SSL/TLS / Manage AutoSSL."
3. Click the "Options" tab.
4. Put a check in the "Allow AutoSSL to replace invalid or expiring non-AutoSSL certificates" checkbox.
5. Click the "Save" button.

Additional resources

Manage AutoSSL: Allow AutoSSL to replace invalid or expiring non-AutoSSL certificates