I don’t know if you can convert that file back to normal, but you can try opening it as utf-8 and save as your system default encoding. Of course, you will need to make backups every time you make experiments. I am sorry for any inconveniences. I hope you have your previous versions of the file. If you use Windows 7, and the documents are in your Documents folder, you should find your backups from Explorer the File properties, Previous versions.
You should always use the latest version of EmEditor, currently EmEditor Professional 10 because there are always bug fixes and improvements.