I’d like to know if the only thing i have to do is remove the lines referring to the commercial SSL certificate.
Run the cerbot command
./certbot-auto certonly --webroot -w /home/domaine/public_html -d www.domaine.com
and add the usual lines of code referring to the Letsencrypt certificate in the vhost file?
You should remove nothing till you issued your cert using the command you posted. Once you get your cert, yes, you can replace the paths of SSL directives SSLCertificateFile and SSLCertificateKeyFile to point to the right paths for your LE issued domains.
As you are using Apache 2.4.10, SSLCertificateFile should point to fullchain.pem file.