For a large mod project I'm working on, I needed to create a valley in a mountain range. So, I went ahead with the landscaping tool and very messily flattened a large swathe of mountains, creating the rough shape for my valley. However, when I went in-game to get a better idea of the size of the valley, all of the existing terrain was still there. If I turned on no-clipping and 'flew' through the original mountain, though, the valley I'd created was still visible behind the original mountain landscape. (Just to clarify, this original mountain was landscape rather than just a mountain object.) I also placed a couple of static objects and they still appear, so my .esp is definitely activated. If it makes any difference, the mod I'm working on has its own .esm.

Here is a picture of the problem, with my valley extending off on the left of the screen.
http://i.imgur.com/f7pxD.jpg

If I continue into the valley though, my landscape edit just cuts off at a certain point, and none of the rest of the valley is rendered. Obviously, in creation kit, none of this mountain is visible.

You need to generate Landscape LOD for your terrain changes. (see Oscape/LOD tutorial A.Velicky did a good tutorial Video for generating LOD, recommended)

http://www.gamesas.com/topic/1386036-video-tutorial-worldspace-lod/

In his tutorial, A.Velicky said that it's only for custom worldspaces - mine is an edit of vanilla Skyrim, although the area I'm editing is technically out of the normal playable area. Can I still use the same technique?

Generally, folk don't make big modifications to the vanilla Tamriel worldspace. If you do make large modifications (like you seem to have done), then you'll have to generate new LOD files to tie in with the area that you've altered.

Are these changes made in the same way as the LOD generation for custom worldspaces, or is there a way to just generate the LOD for a specific area?

you could generate and just keep the coords you need, but as I see you are new to LOD generation and for Vanilla LOD I just would keep my hands off, only bet is to generate the whole LOD for the Tamriel Worldspace ...

Good luck !

I re-generated the LOD for all of Tamriel, and it fixed my problem - my valley displays properly in-game. However, now all static objects in Skyrim pop in from about 10 feet away because I couldn't generate the object LOD (it gave an error when I did this, saying that the _n part of each file should be the same size as the other part, but some of mine aren't for some reason). Anyway, the main problem I have is that when I view the valley in creation kit, despite it looking fine in-game, it's entirely messed up.

In-game part of valley - http://i.imgur.com/0Aa6e.jpg

Same area in creation kit - http://i.imgur.com/LHLBR.jpg

I'm guessing I should just scrap the LOD changes I made, but I'm not entirely sure how to remove them - the changes aren't part of the .esp, so I'm guessing I'll need to re-install Skyrim?

???

No, just delete the files in Data\meshes\Terrain

But that creation kit image looks more like the ESP was messed up somehow, just generating LOD should not cause something like that.

Oh... thanks. I spent ages trying to find the files but didn't think to look there. I was looking for folders called LOD.