0000-default-le-ssl.conf file is generated by
0000-default.conf as a "template".
I would advice to run
certbot again like you did before: it should recognise the presence of a valid certificate and ask you if you'd like to "re-issue" the certificate or just "re-install" the current cert. Choosing the latter should re-generate the
0000-default-le-ssl.conf file again.