Until someone knows how to properly fix this, I have manually edited apache config
In virtualmin / Services / Configure SSL Website / Edit directives
Changed:
SSLCertificateFile /home/api/ssl.cert
SSLCertificateKeyFile /home/api/ssl.key
SSLCACertificateFile /home/api/ssl.ca
to
SSLCertificateFile /etc/letsencrypt/live/api.example.com-0002/cert.pem
SSLCertificateKeyFile /etc/letsencrypt/live/api.example.com-0002/privkey.pem
SSLCertificateChainFile /etc/letsencrypt/live/api.example.com-0002/chain.pem