Let's take a case, you need to use your own NGINX version from the nginx.org repository, but the one from the CloudLinux repository persists.
Please use the priority for Nginx repository, e.g. open the /etc/yum.repos.d/nginx.repo file and add the following into the nginx-stable repo section:
If nothing is set the default priority for repositories is 99. The repositories with the lowest numerical priority number have the highest priority.