What does this re-enabled auto-save feature actually do? I generally just copy the entire server folder to another drive each day.
The world files are stored in their corresponding world folder, but CraftBukkit only saves the changes from the memory to the files on shutdown and on /save-all. If your server suddenly crashed the world would remain how it was the last time it was saved. The auto-save feature let's you periodically save the world to the memory, reducing the damage caused by a potencial crash/failure.