Man this game is a timesink, I spend 15 hours over the last two days on this mess. However the server my friend was hosting decided to nuke our world and we can't find a way to restore it. On the bright side I have incentive to check out the Smogon server now.
First, take the "world" folder that the server makes, and move it somewhere else. Doesn't matter where, just so long as you have a copy of the entire folder somewhere on the computer and it's not where the server file makes it.
Second, run the server file again so it creates a brand new world.
Third, copy or cut all the folders (FOLDERS ONLY, do not copy the three or so files in the main "world" folder) from the original world, the one that you moved, and past them and their contents into the new world. You'll be asked to replace many of the folders. Say yes to all of them and to any files inside the folders that it asks you to replace as well.
And that should be it. I've had my server get corrupted twice due to power failures, and both times I was able to restore it - for the most part - this way. I say "for the most part" because a few chunks will most likely be recreated, effectively erasing whatever was in those spots before. There's nothing you can do about that; if you use a map viewing program - such as Cartography - on the broken world before doing anything, you'll see that those chunks are already replaced. Also, the default spawn area for the server will also change, and unless my server is just weird, this area prevents anyone from destroying or adding blocks to it. This could be a good or bad thing, depending on where it was before and where it moved to.