If you have an Addon Domain set up and would like delete it, please do the following:

1. Login to your cPanel and click Addon Domains.
2. At the bottom, under Actions, click Remove.

Removing the addon domain only removes the domain from the DNS and server configuration. Your files and databases are not deleted or affected by removing the addon domain (other than the fact that you can no longer access the effected files via that domain name).