Hi @2an4,
What is the command you used?.
You shouldn't do that manually. What is the error?.
You don't say what is the client you are using to get your certificates but certbot client has the option --cert-name (since certbot 10.0.0) to issue a cert and replace the old one (to avoid the problem you get about the -000x directory). Anyway, there is no problem if you have a new dir yourdomain-0001, all you need to do is configure your web server to use the new path to the certificate.
To resolve the failed authorization procedure, the first thing you should do is to create the dirs .well-known/acme-challenge/ on your site Document Root. For example, if the document root (the dir that you have configured on your web server) for your domain is /var/www/public_html/yourdomain/ add the dirs to that path so you get /var/www/public_html/yourdomain/.well-known/acme-challenge/.
Once you have the dirs created put a simple test file there:
echo "this is a test" > /var/www/public_html/yourdomain/.well-known/acme-challenge/test
and try to reach it using your browser:
http://yourdomain/.well-known/acme-challenge/test
You should see the text "this is a test", if you get another thing then there is an issue with your conf that should be reviewed. Till you can't see the text, Let's Encrypt couldn't too so you will get the failed authorization message.
Anyway, you said that you were able to issue the cert (no failed authorization error) but then you rename the dirs and now you get this error... are you sure that your web server starts when you renamed the dirs?.
Anyway, you should provide more info about the commands you used, the errors, your web server conf... if you want some help from the community ;).
Cheers,
sahsanu