All you do is read the plugin documentation and see the Admin chat command /home wipe - Removes all homes. and the problem is solved, The plugin is not set to remove the homes after a wipe , As the admin (who stops and starts the server) you have the opportunity of typing that command in chat before anyone else joins or go to NTeleportationHome.json, and depending on your setup the NTeleportationTown.json file and delete all the information in them, if you dont want to join the server,
BUT make sure you delete the data (*not the files) before you start the server, Data files dont always save changes if the plugin is loaded or the server is running,