In order to re-install your server, first login to the control panel.
Navigate to your server and click the More button as pictured below:
** SAVE ANY IMPORTANT FILES BEFORE PROCEEDING
Then, click Reinstall and fill out the following form to your liking.
Your server files will now be deleted and redownloaded using SteamCmd.
** THIS WILL DELETE THE BACKUPS FOLDER AS WELL.
NOTE: It is recommended that you locally save any important files you will need later on by downloading them with FTP before re-installing the server.