The only reference to ca-chain.pem (with a - and not a _) in the Certify the Web documentation is at Deployment Task - Deploy to Apache | Certify The Web Docs.. And that documentation doesn't mention any chain.pem.
So I have no clue what you're talking about exactly.
Also note that the Let's Encrypt ACME server does not provide the root certificate in its chain(s). Nor should any other ACME service. The root CA is present in the applicable root trust store(s) and is not relevant for the webserver. Unless you were talking about the intermediate certificate(s), but that's not the same as the root certificate.