Hardenize.com reports big issue while scanning: "Certificate chain is incorrect. This certificate is delivered as part of an incorrect certificate chain. The problems in the chain render the certificate invalid too. Although some clients (typically browsers) are able to fix or rebuild certificate chains, it's generally not safe to assume that all browsers can."
I'm not 100% sure how acme.sh stores certificates it obtains, but I guess it provided you with cert.pem, chain.pem and fullchain.pem (or something like that). If you are using both SSLCertificateFile and SSLCertificateChainFile directives in your Apache config, you want to use cert.pem and chain.pem respectively. Otherwise, you should use only SSLCertificateFile with fullchain.pem (note that SSLCertificateChainFile is deprecated in Apache 2.4, so you should probably go with second option anyway).
"Fullchain" file is a concatenation of cert and chain files; if you use SSLCertificateFile and SSLCertificateChainFile directives, files specified get concatenated "on the fly" (which leads to chain issues if you happen to set SSLCertficateFile to cert.pem and SSLCertificateChainFile to fullchain.pem).
SSLCertificateChainFile became obsolete with version 2.4.8, when SSLCertificateFile was extended to also load intermediate CA certificates from the server certificate file.
Agreed, if that is being used, then you have probably upgraded the original Apache config well past its' usefulness. SSLCertificateChainFile should not be in use in Apache 2.4.48.
You should review your config for such inconsistencies.
You are truly wizards. Thank you! One error and one depreciated configuration solved!
I've now set SSLCertificateFile to point to the fullchain file and removed the use of SSLCertificateChainFile altogether. As you correctly pointed out this config is not new, it has evolved the last 10-20 years, I believe . My Apache config is now as follows;