say you have a waypoint in the overworld there would be a button in ur edit section that lets you make a copy of your waypoint for the nether auto changes the cords for you.

I recommend using the Prefer Overworld Waypoints setting in XaeroPlus.

it will make it so waypoints are shown in both OW/nether and but stored only in overworld coordinates. so it kinda prevents this problem from occurring in the first place.

i'll leave this feature request issue open but i probably won't get to it anytime soon