Oi vey… What a drag… I’ve made an apparently dumb mistake I’d like to share in the hopes I may help prevent others doing the same.
If you Duplicate your scene to alter the terrain, you will be altering the same terrain asset from the level you duplicated. It is not a copy, despite first appearances.
You’ll need to also duplicate the “terrain data” asset, and make sure each scene is pointing to it’s own terrain data. I lost a lot of work assuming my not-prefab terrain-dupe was a real duplicate, only to find when I made my 2nd (and third, oh my) scenes I was always modifying the same root asset… Not too funny, Unity.