Hi, I would recommend to use another apache config file for your nextcloud site - then it will be easier to manage, and less risk of mixing up content between the sites. certbot will also be able to find and generate for both sites if you use different config files.
To do this, copy the 000-default.conf file to a new one, f.ex cloud.mydomain.me.conf. On debian/ubuntu type systems you should do that in the /etc/apache2/sites-available directory.
Change the ServerName in each config file so apache knows which config to use for the sites:
ServerName mydomain.me (in 000-default.conf)
ServerName cloud.mydomain.me (in cloud.mydomain.me.conf)
I would also recommend to make another DocumenRoot for the nextcloud site, to avoid mixup - fex /var/www/cloud.mydomain.me or /var/www/nextcloud (remember to move or reinstall the nextcloud files there as well)
You can add some more apache settings to make nextcloud work from the root (instead of /nextcloud) - see the install guide for further info on this and some other tips:
Remember to activate the new site by running: a2ensite cloud.mydomain.me
In DNS just add a cname for cloud.mydomain.me, pointing at you current dns name (or use A record pointing to the IP)
Now you can run certbot again and it should find both sites, if you got the configs correct.
Nextcloud will usually figure out most of the site settings automagically, but if needed you can use ‘overwrite.cli.url’ and some other related ones to make sure it knows which site URL to use. Don’t use the IP address anymore, as it will use the default apache config.
Hope that helps, good luck further on!
btw sqlite3 is very weak, use my/mariasql instead if you start using your cloud 