The old tree snapping mod does not save the Y position of trees, and simply re-routes the way trees are positioned on the map. If you load these maps for the first time using my mod, the trees are bound to be repositioned. They could either be in their original position, fly again, or be positioned at terrain level, or in certain cases be positioned below the terrain. It is totally random.
You will need to reposition these trees using my mod, then save it for the position to persist.