The domain in NodeJS creates an apache/nginx configuration that forwards we requests to the Node App. If you created the NodeJS app using your main domain, Node overwrote your config file in apache for your website. Here should be your steps to fix the issue.
1) Update the hostname as you have for nodeJS. Make sure that your Node Webapp is available from this new URL.
2) Go the the root CWP Panel -> WebServer Settings -> Webservers Main Config
3) At the bottom, Click rebuild all vhosts on save
4) Click save