The only alternative I can think of is that your file was encoded with ANSI, but now the editor thinks it is UTF-8. You can try opening these files in Notepad++ and see if messing with the encoding gets you closer to your original file.
And how to prevent this? Regular backups. There is a common wisdom that anything without a backup is not important. The absolute best practice is to have backups to 2 different off-site places (e.g. cloud storage), preferably on different continents and in different formats.
As to why this might have happened: it is impossible to tell from your description. We don't know your OS, your hardware, or even your Matlab version (other than that it is at least R2006a, since you can't change the editor colors in the way you did prior to that). Even if you did provide that information I couldn't tell you, because it isn't my area of expertise.
