Well, I suppose I'll start from the beginning.
I made the height map and mask correctly (I have made plenty so I'm not too... nooby haha) and put all the objects in. While I was finishing up putting objects in the map, I decided to touch up the height map to better fit my picture of the place. Map Maker accepted the new heightmap (just an updated version of the same one from before) perfectly, but then I saved it and check it in cape. The first height map was there, but not the updated version. So I went to map maker and exported the map with the same result. It hasn't changed.
Although, I /did/ look into the map folder in FeralHeart>Media>Terrains and it has the "MapnameTerrain" notepad file (as well as all the others) I opened that and check inside, and maybe I need to just change that? I wouldn't be entirely sure how to, if that is what this requires.