I'm not sure which plugin you are using for your server, but if anything I would recommend switching to a new world creation plugin.
http://dev.bukkit.org/bukkit-plugins/multiverse-core/
All you have to do for generating a world is type
/mv create [Name] normal
Then it generates the world into your main server folder. When you open the folder of the new world delete all the files inside it, and replace them with new ones, then restart your server. Then type /mv tp [world name] or type /mv list to teleport to the world you created.