Now is the strangest part... I fixed each and every broken symlink. Now there are no more symlink errors, yet when i go to renew a domain, it gives the same error... 
root@localhost:/etc/nginx# certbot renew --dry-run --cert-name www.theflowershop.ie
Saving debug log to /var/log/letsencrypt/letsencrypt.log
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Processing /etc/letsencrypt/renewal/www.theflowershop.ie.conf
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Simulating renewal of an existing certificate for www.theflowershop.ie
Certbot failed to authenticate some domains (authenticator: nginx). The Certificate Authority reported these problems:
Domain: www.theflowershop.ie
Type: unauthorized
Detail: 178.79.159.104: Invalid response from https://theflowershop.ie/: "\n<!DOCTYPE html>\n<html lang=\"en\">\n\n\n\n<head>\n <meta charset=\"utf-8\">\n <meta name=\"viewport\" content=\"width=device-width, initia"
Hint: The Certificate Authority failed to verify the temporary nginx configuration changes made by Certbot. Ensure the listed domains point to this nginx server and that it is accessible from the internet.
Failed to renew certificate www.theflowershop.ie with error: Some challenges have failed.
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All simulated renewals failed. The following certificates could not be renewed:
/etc/letsencrypt/live/www.theflowershop.ie/fullchain.pem (failure)
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1 renew failure(s), 0 parse failure(s)
Ask for help or search for solutions at https://community.letsencrypt.org. See the logfile /var/log/letsencrypt/letsencrypt.log or re-run Certbot with -v for more details.