[BlueOnyx:21744] Letsencrypt update has stopped SSL working

[Colin Jack]

We have a site that has been successfully using an LE cert for some time.
I received an email from LE saying it was going to expire (even though it was on auto-renew) so I renewed it manually using the GUI:

2018-02-14 08:02:15,153:DEBUG:certbot.storage:Writing new private key to /etc/letsencrypt/archive/www.cmt-london.co.uk/privkey2.pem.
2018-02-14 08:02:15,153:DEBUG:certbot.storage:Writing certificate to /etc/letsencrypt/archive/www.cmt-london.co.uk/cert2.pem.
2018-02-14 08:02:15,153:DEBUG:certbot.storage:Writing chain to /etc/letsencrypt/archive/www.cmt-london.co.uk/chain2.pem.
2018-02-14 08:02:15,154:DEBUG:certbot.storage:Writing full chain to /etc/letsencrypt/archive/www.cmt-london.co.uk/fullchain2.pem.
2018-02-14 08:02:17,601:DEBUG:certbot.storage:Writing new config /etc/letsencrypt/renewal/www.cmt-london.co.uk.conf.new.
2018-02-14 08:02:17,610:DEBUG:certbot.reporter:Reporting to user: Congratulations! Your certificate and chain have been saved at /etc/letsencrypt/live/www.cmt-london.co.uk/fullchain.pem. Your cert will expire on 2018-05-15. To obtain a new or tweaked version of this certificate in the future, simply run letsencrypt-auto again. To non-interactively renew *all* of your certificates, run "letsencrypt-auto renew"

GUI shows everything as it should be but website is now showing invalid cert warning:

www.cmt-london.co.uk uses an invalid security certificate. The certificate is only valid for the following names: *.mainline.co.uk, mainline.co.uk

If I continue (add exception or click advanced in chrome) it goes through  to the SSL cert for the server rather than the vsite (hence the cert mismatch).

How can I fix this please?

Thanks

Colin