As you are using Apache, as @rg305 said, you can add an Alias directive to your main Apache conf so ALL the requests to
http://anyofyourdomains.tld/.well-known/acme-challenge/whatever will be directed to another directory in your server instead of use the document root of your domain.
Following @rg305 example:
You could create
/var/www/letsencrypt/ and use it as the dir to redirect all the challenge requests for your domains so you should add this line to your main apache conf file.
Alias /.well-known/acme-challenge/ /var/www/letsencrypt/.well-known/acme-challenge/
After reload/restart Apache you should test wheteher it is working or not with your domains, create a test file and check whether you can access it.
echo "This is a test" > /var/www/letsencrypt/.well-known/acme-challenge/test
And now try to access the test file: http://yourdomain.tld/.well-known/acme-challenge/test
if it works, you must use
/var/www/letsencrypt/ as webroot when issuing new certificates and also, if you already issued certificates for your domains, you should modify their renewal conf file located here
/etc/letsencrypt/renewal/ and change the webroot map for your domains to point to
/var/www/letsencrypt/ instead of their document root.
Anyway, instead of using the Alias in the main Apache conf file, you could use it only in the VirtualHost section of the problematic domains so it will only affect that domain/domains that belongs to that VirtualHost section.