Normally whenever you run a server and a file is missing from the Craftbukkit folder, it automatically regenerates a new one, like said above. This happens with me now and then, when upon entering the end there is nothing. If that's what you mean. The chunks simply don't load but just try a few times. EDIT: I don't think taking somebody else's end file will do anything but generate a different terrain. It probably won't fix your problem.
rename the original map name. (example: world to servermap) or just enter the end and force it to create the file