Messed up nginx configuration after deleting some certificates and now nginx wont start so I can't renew my certificates

[Yiannis128]

I accidentally made multiple certificates with the same domain (while I was learning how to use the program). After that I deleted the certificates using certbot delete and now when I run the command below it gives me an error.

My domain is: yiannis-charalambous.com

I ran this command: certbot --nginx -d yiannis-charalambous.com,www.yiannis-charalambous.com,muc.yiannis-charalambous.com,upload.yiannis-charalambous.com

It produced this output:

Saving debug log to /var/log/letsencrypt/letsencrypt.log
Error while running nginx -c /etc/nginx/nginx.conf -t.

nginx: [emerg] BIO_new_file("/etc/letsencrypt/live/muc.yiannis-charalambous.com/fullchain.pem") failed (SSL: error:02001002:system library:fopen:No such file or directory:fopen('/etc/letsencrypt/live/muc.yiannis-charalambous.com/fullchain.pem','r') error:2006D080:BIO routines:BIO_new_file:no such file)
nginx: configuration file /etc/nginx/nginx.conf test failed

The nginx plugin is not working; there may be problems with your existing configuration.
The error was: MisconfigurationError('Error while running nginx -c /etc/nginx/nginx.conf -t.\n\nnginx: [emerg] BIO_new_file("/etc/letsencrypt/live/muc.yiannis-charalambous.com/fullchain.pem") failed (SSL: error:02001002:system library:fopen:No such file or directory:fopen(\'/etc/letsencrypt/live/muc.yiannis-charalambous.com/fullchain.pem\',\'r\') error:2006D080:BIO routines:BIO_new_file:no such file)\nnginx: configuration file /etc/nginx/nginx.conf test failed\n')

My web server is (include version): nginx version: nginx/1.14.2

The operating system my web server runs on is (include version): Debian 4.19.181-1

My hosting provider, if applicable, is:

I can login to a root shell on my machine (yes or no, or I don't know): yes

I'm using a control panel to manage my site (no, or provide the name and version of the control panel): no

The version of my client is (e.g. output of certbot --version or certbot-auto --version if you're using Certbot): certbot 0.31.0

[Yiannis128]

Fixed this by going into /etc/nginx/sites-available/default and deleting all the things made by certbot (they were commented). Then restarted nginx and everything was fine.

[rg305]

I'm left wondering exactly how you deleted the certificates and what state certbot is in at this time...
If you don't mind, please show the output of:
certbot certificates

[Yiannis128]

It seems to be fine now.

Saving debug log to /var/log/letsencrypt/letsencrypt.log

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Found the following certs:
  Certificate Name: yiannis-charalambous.com
    Domains: yiannis-charalambous.com muc.yiannis-charalambous.com upload.yiannis-charalambous.com www.yiannis-charalambous.com
    Expiry Date: 2021-11-27 15:46:39+00:00 (VALID: 89 days)
    Certificate Path: /etc/letsencrypt/live/yiannis-charalambous.com/fullchain.pem
    Private Key Path: /etc/letsencrypt/live/yiannis-charalambous.com/privkey.pem
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[rg305]

Excellent.