[KWo]

Any change in waypoints (no matter - if that is only a move of the waypoint in the new place or if You are deleting the waypoint) ask You - at the end of editing - to save waypoint configuration file - map_name.pwf. Then after saving the *.pwf file the server is restarting the map. At the map loading there is a an automatically check - if the pwf file is newer than *.pvi (visibility table) / *.pxp (experience table) files - those files are deleted and automatically created new ones. So You don't need to do anything if You are just editing *.wpf files.
The only problem is - if You had Your *.pwf file, You were playing on the map and there are now some *.pvi / *.pxp files as result of using Your *.pwf file and playing on the map, then - You are replacing Your *.pwf file by another one (downloaded from the internet or taken from Your friend) - and the time stamp of the creation/modification is older than Your pxp / pvi files and - number of waypoints used on that file is equal to number of waypoints in Your previous *.pwf file. In that case the system is not able to recognize Your pxp and pvi are wrong - so You need to delete them manually. So - as a rule - You should always do so - when You are taking some waypoints from the internet or from someone's else, You should always delete coresponding *.pvi and *.pxp files. In other cases You don't need to take care about those files.