Have you tried MCEdit? It's a graphic world editing program. It's a pretty straight forward matter to delete unused chunks and you can see what you're deleting so there's no feat of accidentally erasing any projects. I used it back when the biomes changed and my main fortress found itself in a winter zone and it's interior moat froze over. I moved the whole thing (right down to the bedrock) clear across the map into a newly generated temperate zone.