Yes, if you delete the folder "Journeymap" inside your modpack folder, it will be re-created when you load up your world. Obviously you will lose all your saved waypoints and all the explored areas will return to "blacked out", but I'm sure that's obvious. You'll just have to re-explore everything.
Mapwriter and journeymap both, iirc, store SMP map data using the server name as a sub folder of their folder in saves.
If you want new maps on the same server you need to rename the server entry.