I don't get any Letsencrypt certificates anymore (challenge did not pass)

Hi all,
Webmin, apache and Letsencrypt worked fine a year ago and now I reactivated everything and I just don’t get any certificates anymore.
I followed tutorials, forum advices but whatever I do I have not any success. Please! Can someone guide me through this?

So I have the domain rootshape.com. And I have a subdomain cloud.rootshape.com on the same server with the same ip. The cloud.rootshape.com root folder is inside the rootshape.com root folder.
Right now I disabled the port 80 virtual hosts so I have only port 443 for rootshape.com and cloud.rootshape.com but I cannot access them without certificate (SSL record too long error)
After I went to webmin config -> SSL -> Letsencrypt, I tried all options in all combinations (DNS, apache matching hostname, etc.)
Once I succeeded in getting a certificate for rootshape.com only, but I don’t know what I have changed because it didn’t work a second time. (I lost the certificate for rootshape.com right after I tried to get one for cloud.rootshape.com in a seperate process)

So, in my last try to get a certificate, I tried to get a certificate by folder for rootshape.com, cloud.rootshape.com and I got the error:
cloud.rootshape.com challenge did not pass: Invalid response from http://cloud.rootshape.com/.well-known/acme-challenge/_9y9oRX8ZGhXSW3E87IpaZHloo9S70aehGR215inzYQ:

I have updated webmin to the most recent version (1.900) and I updated and upgraded and dist-updated everything else, too. I have Raspbian Linux 9 running.
I hope so much that someone can help me because I have totally no idea what I could do.

Check your httpd conf file and make sure you have a ServerAlias set up for you domains i.e.

ServerAlias www.rootshape.com
ServerAlias cloud.rootshape.com (depending on how your server is configured)

Hi, thanks for your answer and Merry Christmas.
Depending on how my server is configured?
I have a ServerAlias written into the conf file, of course (webmin created these conf files by default, am I right?)
Anyway, I installed certbot and got my keys pretty easy by that using the command:
sudo certbot certonly --webroot -w /var/www/ -d rootshape.com -w /var/www/cloud/ -d cloud.rootshape.com
I will add the key to my virtual hosts after christmas and add a cronjob running the command “certbot renew” every two months. I hope that will work