The release of alpha 3 QuArK level editor, makes you the user able to modify the waypoints properly. Fix bad links and and move bad placed nodes without starting from scratch. You can edit their flags setting, if they are to be a ladder , water or a normal move waypoint.
The waypoint editor:
I have also started a comunity page, where i will update the editor above to also work with the future releases.
Go on to Franva.org and register! You will get the chance to test my latest bot versions aswell as QuArK map editor releases before they are aviable from the oficial page.