@Denniskoch Can you check if this file is present on your server?

/etc/nginx/ploi/yourdomain.com/server/disable-basic-auth-well-known.conf

(Replace yourdomain.com with the domain you're having issues with)

There is only a auth.conf. I checked another site which has the correct file in there. I also tried removing auth and adding the user again, and removing SSL and adding a new certificate. Both worked but didn't create the corresponding conf file.

Is that domain a fairly old domain created via Ploi? If you can, create that file I mentioned above with these contents and restart NGINX:

# This location allows the SSL requests and renewals by Certbot & Let's Encrypt to go through.
# If you're not comfortable with this setting, you may remove this file and restart NGINX.
location /.well-known/ {
	auth_basic off;
}

The domain shouldn't be that old. Less than half a year. Copied that file over from another site.

Is it possible for you to try or test this again with a fresh domain (or testing subdomain)? It should've been fixed by now.