By default, the Minecraft server does not have any files. To reset your server back to default, you would delete everything on it.
The quickest way to delete everything is to use the setup option to delete all the server files.
Login to the Minecraft control panel and navigate to your server's control panel.
Stop the server
Click on the Files option on the left-hand side
Click on the Setup option
Select the "Clear Mod directories and Plugins" option from the Template dropdown list.
Enable the "Delete All Server Files" option
Enter in your Minecraft control panel password into the Password field
Click Apply
When you next start the server, all the files will be deleted (including backups).
