If your website is down because of an expired certificate and it’s behind Cloudflare - assuming you haven’t uploaded the expired certificate to Cloudflare itself, which isn’t even an option with their free service - you could just temporarily switch back to “Full SSL” mode (rather than “Full SSL (Strict)”) to get your site back up while you fix the certificate.
I don’t think an expired certificate would cause Cloudflare to render an <iframe> pointing to GoDaddy, though. Are you sure it’s the certificate that expired, and not the domain itself?