Removing the ProtectionAreas.sqlite file (while the server is not running) will do the trick. The plugin will re-create an empty file afterwards.
Alternatively, you could open the file in sqlite browser and remove all records in it; this would work even while the server is running (but it may take a while until the changes are reflected to the game).
Alternatively, you could open the file in sqlite browser and remove all records in it; this would work even while the server is running (but it may take a while until the changes are reflected to the game).