You can reset the server back to it's default/new state by shutting the server down, logging into the server files via the FTP and then select and delete everything. If you need to keep anything for future use, such as world folders, make sure to download them first as they cannot be recovered once they are deleted.
Once everything has been deleted simply select the server version you wish to use on the list on the control panel and then start the server back up!

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How to Reset Your MineCraft Server
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