Yeah, you should always watch out for a crapper in the mission file... Ive seen this too, but with bricks. If you save a map with bricks on it, it gets saved into the .mis file (even ghost bricks). This was such a problem one map wouldn't work, and when I went in to clean it up it consisted of my 1000 bricks (of course) and each one was made up of 5-7 lines. So ya, I dragged and held for a long time to get rid of all those crap objects.
I think this was how my first Paradise Island (the remake of which is Shipwreck Island) got it's terrain removed - I was clearing the trees in such a manner and overlooked the fact that I had highlighted the terrain object as well... oh well, it's remade now ;)