To either fully wipe your Rust server or wipe blueprints only, you will need to login to your server through FTP. You may found a download link for WinSCP here: http://winscp.net/eng/download.php
Stop your server from the panel
Log in to FTP using WinSCP (a free FTP software) using the connection details found in the "FTP Details" section of the game server control panel
Navigate to the directory you wish to upload or edit a file.
To wipe blueprints only, delete the following file:
/server/experimental/player.blueprints.3.db
To wipe the entire server, delete the entire server following folder found at the top level.
Once you are done, restart your game server.
If you run into any issues with this method please let us know by submitting a support ticket!