Only the domain's DNS and server configuration will be deleted when the addon domain is deleted. The files and databases on the removed domain remain unaffected. You can still view the affected files in your File Manager even though you can no longer access them through the removed domain name.
CPANEL
To remove an addon domain in cPanel:
STEP 1: In the Domains section, locate the addon domain you wish to remove, then select Manage.
STEP 2: Click the tab labeled “Remove Domain.”
STEP 3: To proceed, select “Yes, Remove This Domain.”
The domain will no longer be shown in the Domains section of your cPanel.