I'm having the same issue, but using apache. Certbot gets a 404 error when trying to load the acme-challenge. Certbot worked before and I haven't changed the apache configuration, but I'm going to check through it.
I was able to get my renewal to work by specifying where my document root was with this parameter:
--webroot -w /var/www/html
Hi @Addy771, welcome to the LE community forum 
Although I am glad you were able to circumvent the problem and get a new cert issued, the problem is likely still there and should be corrected.
If you would like to go down that road, please show the output of:
sudo apachectl -t -D DUMP_VHOSTS
Thanks @rg305! I am indeed interested in what the root cause of this problem is.
The output of sudo apachectl -y -D DUMP_VHOSTS:
[Mon Sep 20 15:32:17.374292 2021] [core:error] [pid 13405] (EAI 2)Name or service not known: AH00547: Could not resolve host name doc.chtech.us.to -- ignoring!
AH00558: apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1. Set the 'ServerName' directive globally to suppress this message
VirtualHost configuration:
24.84.228.171:80 S0106749be8129543.vc.shawcable.net (/etc/apache2/sites-enabled/cht-server.conf:6)
*:443 chtech.us.to (/etc/apache2/sites-enabled/cht-server-le-ssl.conf:2)
I hadn't noticed that ServerName was missing.
You can basically ignore this (warning):
This one is a bit more severe:
[if you are trying to serve that FQDN]
So, which is the FQDN that you are having trouble with?
chtech.us.to ?
doc.chtech.us.to was left in by mistake, I've removed it now. chtech.us.to is what I was having trouble with.
OK, chtech.us.to lacks a vhost config for port 80.
Did you disable it? or delete it?
We should have a look at file:
/etc/apache2/sites-enabled/cht-server.conf
cht-server.conf:
<VirtualHost chtech.us.to:80>
# The ServerName directive sets the request scheme, hostname and port that
# the server uses to identify itself. This is used when creating
# redirection URLs. In the context of virtual hosts, the ServerName
# specifies what hostname must appear in the request's Host: header to
# match this virtual host. For the default virtual host (this file) this
# value is not decisive as it is used as a last resort host regardless.
# However, you must set it for any further virtual host explicitly.
#ServerName www.example.com
ServerAdmin webmaster@localhost
DocumentRoot /var/www/html
# Available loglevels: trace8, ..., trace1, debug, info, notice, warn,
# error, crit, alert, emerg.
# It is also possible to configure the loglevel for particular
# modules, e.g.
#LogLevel info ssl:warn
ErrorLog ${APACHE_LOG_DIR}/error.log
CustomLog ${APACHE_LOG_DIR}/access.log combined
# For most configuration files from conf-available/, which are
# enabled or disabled at a global level, it is possible to
# include a line for only one particular virtual host. For example the
# following line enables the CGI configuration for this host only
# after it has been globally disabled with "a2disconf".
#Include conf-available/serve-cgi-bin.conf
# Redirect to HTTPS
RewriteEngine on
RewriteCond %{SERVER_NAME} =chtech.us.to
RewriteRule ^ https://%{SERVER_NAME}%{REQUEST_URI} [END,NE,R=permanent]
</VirtualHost>
Now when I do a dry run without specifying the web root, it's successful
adam@CHT-server:~$ sudo certbot renew --dry-run
[sudo] password for adam:
Saving debug log to /var/log/letsencrypt/letsencrypt.log
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Processing /etc/letsencrypt/renewal/chtech.us.to.conf
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Simulating renewal of an existing certificate for chtech.us.to
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Congratulations, all simulated renewals succeeded:
/etc/letsencrypt/live/chtech.us.to/fullchain.pem (success)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
It doesn't seem like the problem exists anymore.
That vhost config lacks a ServerName.
Thanks, I fixed that.
OK, so is everything good now?
Yes, other than my HTTPS redirect not working.
At first I had
RewriteEngine on
RewriteCond %{SERVER_NAME} =chtech.us.to
RewriteRule ^ https://%{SERVER_NAME}%{REQUEST_URI} [END,NE,R=permanent]
I also tried
RewriteEngine on
RewriteCond %{HTTPS} !=on
RewriteRule ^/?(.*) https://%{SERVER_NAME}/$1 [R=301,L]
as well as
Redirect / https://chtech.us.to/
But none of these seem to work. The rewrite module is enabled, not sure what's going on.
I dare say Apache is going on!
Let's (re)review the output of:
sudo apachectl -t -D DUMP_VHOSTS
VirtualHost configuration:
24.84.228.171:80 chtech.us.to (/etc/apache2/sites-enabled/cht-server.conf:3)
*:443 chtech.us.to (/etc/apache2/sites-enabled/cht-server-le-ssl.conf:2)
I changed the vhost to *:80 instead of chtech.us.to:80 and now the redirect is working. Thanks again for your guidance!
So if now all is good, then I'm glad to have helped you get there 
Cheers from Miami 
#FreeCUBA 
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