When you proxy your site through cloudflare it allocates a certificate to use automatically, but you have also at some point configured your web server to have a certificate using certbot-auto. This would let you access your site using https when not using cloudflare.
So the email you got is telling you the certbot-auto app isn't supported on your linux distribution anymore and you should change to using certbot. There is more information here: Certbot-auto no longer works on Debian based systems - #7 by bmw
Note that even if your server certificate expires your Cloudflare proxying may continue working depending on which SSL settings you have enabled in Cloudflare.
The problems loading stylesheets are because of your content management system settings and are not related to renewing your certificate. It looks like you've maybe fixed that already.