Then I guess I've got egg on my face but I think I've figured it out.
I don't download directly onto my gaming PC, I use a laptop at work and then copy across. I have done a fresh install on my laptop recently, but because I can't access my programs folder over the network, I have to copy it to my (laptop) user folder and then onto my main computer. At some point it must have overwritten an existing copy (most likely when I copied it to the user folder on the laptop since the Caucasus are there too) or merged with files that weren't deleted as skate said.
In my memory it was pointed out ages ago in a thread that the map was natively accessible by opening a new map in the mission editor. I know I haven't knowingly modded it in because I don't actually know how to mod it in (I've always just assumed that it worked for everyone), but I have long in the past experimented with copying across the whole 1.5 folder to decrease download size when installing 2.0 and then running the update command followed by the repair command in the updater (I know I don't need to do that now since DCS automatically finds the existing files).