Baking Weirdness

[Teric neDhalir]

Here's something I've never seen before....
I've done some work on an existing area - changed terrain, texturing, added water - but the changes do not show up when I run the mod. The weird thing is that if I export the area, import it to a new module and run it (without baking again) the changes are visible. How can it have two versions of the same .trn/.trx files at once?? I should mention that the walkable area is correct it's just the change in height and texture that you can't see.
Anyone seen anything similar and know how to fix it?
Teric