How to Remove an Addon Domain from cPanel?

Go to cPanel.

Click the Addon Domains button in the Domains section:

On the next page, you will see all your Addon domains listed. Click the Remove link beside the domain you want to be deleted:

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On the Addon Domain Removal screen, you will see a message similar to this: "Are you sure you wish to permanently remove the addon domain “example.com”?" 

After you remove the addon domain, it will only be removed from the DNS and server configuration. Removing the addon will not affect or delete your files and databases (other than the fact that you won't be able to access the affected files via that domain name).