When you use the Terrain editor.. and then refresh the map.. does any other terrains go back to normal or stay how you had them.. and only the tiles you edited change?

Terrain edits aren't preserved by the refresh script. The refresh resets all the terrain back to the base map that you've installed.
There are workarounds however, such as using admin lands and temporary GM guild claims. Since the last FeudalTools update you can also use the image exporter to export the current state of the map (including all edits) and forge a new custom map with it.