I've tried walking all around and even parachuting from the above cliffside, but it still won't show up as discovered.
Actually, after some investigation, it looks as if the icon simply does not change to transparent once located. I've been to a few more duck locations including some I had never been to before and they just didn't change on the map.
White-Tailed Deer south of Joseph's compound has this issue too
In the Image the icon has a brown outline which means it was discovered already.