When deleting a file using the cPanel File Manager, by default it will be placed in the .trash folder in the account's home directory. The instructions below cover how to remove these files from the server completely.
1) Login to cPanel for the account and navigate to the following location.
cPanel > Files > File Manager
2) Click the "View Trash" button.
3) Click the "Empty Trash" button.
4) Confirm by clicking the "Empty Trash" button in the pop-up box.