This script substantially reduces the size of large Minecraft worlds with the help of LogBlock. Mine dropped from 11gb to 2.7gb and everything is 100% the same as it was before.
The way it works is it prunes Minecraft regions that have no LogBlock history. It doesn't delete any files and only copies them to a new directory. You can then test the new region folder and eventually replace your existing folder. I do suggest keeping the original as a backup just in case something goes wrong.
You need to set the parameters to connect to your LogBlock database and you need to set the source and destination directories.
This requires PHP and once configured is only a single command:
php logblock_world_pruner.php