The server ran out of memory so I transferred it all to a new server, added a 2nd drive and transferred it all back, I used rsync to move the data back and forth. Could this have done something to it? How do I fix whatever the error is?
Just from googling around it could also be some corrupted chunks in the world. (Source here and here)
As a test, generate a new world to see if the server boots (make sure to backup the existing world)
If the server boots cleanly you could try something like minecraft region fixer on your existing world. Although I've never used it myself, just make sure to keep a backup.
I tried a new world and it worked but I need this world so is there a way to do everything server side? The world is about 40GB[DOUBLEPOST=1378333950][/DOUBLEPOST]If this helps at all the server doesn't even start or load all the plugins, crashes during boot up.
I think your issue is perfectly recoverable. It's just some corruption relating to ender storage which I don't have the expertise to figure out exactly what it is unfortunately.
Ok I removed several things from the world (no region files) just things like chunkloader data and endertank data and now I get this crash report http://pastebin.com/fSF0rRw4. still crashes on startup