I checked permissions and ran it again and it still erased my .points file when I went to create a new waypoint (and then it wouldn't save that waypoint). I restarted it with just a blank .points file and it was able to save new WPs without issue, and then load those WPs and allow me to add new ones after restarting again. It just seems to take issue with WPs created by an older version?
Would it help if I sent you the .points file? Or the whole VoxelMods folder?