I don't think you can fix them without generating new terrain, sadly. This problem can also pop up if you use plains or forest as base terrain, then add large patches of village or path texture, which can look fugly with green or brown tints baked in the terrain. I tried to color those spots with complementary colors to get white (no tint) again, but I never managed to make it disappear completely, just make it a bit less obvious. You can try painting a magenta color over the green tints, maybe it will help.
Another big problem with pregenerated terrain are some kinds of vegetation. Namely, the bigger kind. Grass, you can remove by painting textures over. Trees or bushes, not. That's why in some of my maps there are bushes in the middle of a plaza. In Greipenfurt castle, one bush was enraging me so much that I lowered it into a small pit and covered it with a boxing ring.
The only way you can completely get rid of this problem that i know of is by starting with completely flat snow terrain, then shaping the terrain, painting tints+textures, and placing vegetation all by hand. It's a hell of a pain, though. Also, I'm not sure if placing vegetation by hand results in the map running at lower fps, which could very well be possible.
