• Back up the account in question before making any changes.
• In the account’s cPanel, remove the addon domain. This will not remove the subdirectory that contains the addon domain’s site content.
• In the WebHost Manager, use Main >> Account Functions >> Modify an Account to change the domain name associated with the account in question.
• Move your site content from the addon domain’s subdirectory to the public_html directory.
• Recreate any e-mail addresses and FTP users that belong to the domain that was the addon domain.

https://forums.cpanel.net/threads/how-to-replace-main-domain-in-cpanel.165158/

Please keep in mind that changing your Primary Domain will have other effects on the account, which have been outlined below:

• Email – All of the email accounts created for domainA.com will turn into @domainB.com accounts. You@domainA.com will now be You@domainB.com. If you still needed You@domainA.com then you will need to add domainA.com to your CPanel again as either a parked or addon domain name and recreate the email account.
• Files – If domainB.com was an addon domain name and all of the files were located in public_html/domainB, you will need to re-upload or move the files to public_html.
• Subdomains – All of your subdomains.domainA.com will turn into subdomains.domainB.com.
• Search Engine Results impact – When you are changing the main domain on your account, be aware that you can affect the search engine rankings of the website. You can take this into account by creating 301 re-directs and also by updating the preferred domain setting in the search engine (as per Google’s article under Webmaster Tools: 301 redirects).

http://www.webhostinghub.com/help/learn/domain-names/general-faq/change-the-main-domain-name

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