If you upgrade an ESXi host to ESXi 6.0 or later, the upgrade process replaces the self-signed (thumbprint) certificates with VMCA-signed certificates. If the ESXi host uses custom certificates, the upgrade process retains those certificates even if those certificates are expired or invalid.

If you decide not to upgrade your hosts to ESXi 6.0 or later, the hosts retain the certificates that they are currently using even if the host is managed by a vCenter Server system that uses VMCA certificates.

The recommended upgrade workflow depends on the current certificates.
Host Provisioned with Thumbprint Certificates
If your host is currently using thumbprint certificates, it is automatically assigned VMCA certificates as part of the upgrade process.
Note: You cannot provision legacy hosts with VMCA certificates. You must upgrade those hosts to ESXi 6.0 later.
Host Provisioned with Custom Certificates
If your host is provisioned with custom certificates, usually third-party CA-signed certificates, those certificates remain in place during upgrade. Change the certificate mode to Custom to ensure that the certificates are not replaced accidentally during a certificate refresh later.
Note: If your environment is in VMCA mode, and you refresh the certificates from the vSphere Web Client, any existing certificates are replaced with certificates that are signed by VMCA.

Going forward, vCenter Server monitors the certificates and displays information, for example, about certificate expiration, in the vSphere Web Client.

Hosts Provisioned with Auto Deploy
Hosts that are being provisioned by Auto Deploy are always assigned new certificates when they are first booted with ESXi 6.0 or later software. When you upgrade a host that is provisioned by Auto Deploy, the Auto Deploy server generates a certificate signing request (CSR) for the host and submits it to VMCA. VMCA stores the signed certificate for the host. When the Auto Deploy server provisions the host, it retrieves the certificate from VMCA and includes it as part of the provisioning process.
You can use Auto Deploy with custom certificates.