This happens when both the current CA certificate that is expiring or already expired, and the new certificate have the same Subject Key Identifier hash on them.
To fix, the expired or expiring certificate needs to be removed from the certificate trust store.
To remove, either use vCert tool or, Removing CA Certificates from the TRUSTED_ROOTS store in the VMware Endpoint Certificate Store(VECS).
Once removed, import the new certificate using vCert or through the vSphere Client UI Certificate Management.