Does it??
If true, that would indicate that the game is running the elevation solver every time the scenario is loaded, and the scenario file is only saving the fixed/direct elevation points. Which doesn't seem like a very good design.
The alternative would be for the scenario file to store the elevation of every individual square. The elevation solver runs in the map editor every time you make a change anyway, so why not store those already solved values? Even on a large map, it's not a lot of data. The trade off between processing power/time vs storage doesn't seem to make sense to recalculate every time it loads. But I could be wrong in that design choice.