Maybe you accidently deleted some file from directory with scene files ? Please check that you have 256 files in that directory. Also, please write what tool you're using to extract and repack archive.
No, section files aren't important, you should delete them.
Scene Edit couldn't mess this up, because it's editing only one file at time, and you talking about monsters that are in diffrent files: Zenene is in file no. 114, Sample:H0512 - 115, Heli Gunner - 116.