You are able to swap main domain name through whm check following steps.

whm >> Account Information >> list accounts >> select current main domain name. go to username column click on icon  add new domain name in text box against domain click on save .

Domain name is changed for your account. Now you are unable to view previous subdomains in cpanel, to solve this issue you have to update new domain name in /var/cpanel/users/username
e.g. Suppose you have swap the domain name from abc.com >> xyz.com

now your existing subdomain pp.abc.com is inaccessible to access same sub domain you have to change the domain name as per below pp.abc.com >> pp.xyz.com  in /var/cpanel/users/username . Also change the domain name as per above in virtual host entry under httpd.conf file. Restart the http service. Now you are able to access subdomain pp.xyz.com.