I haven't payed attention to this, but if a mod screws up something and resets the
options.dat file, maybe it also resets the
unlocked.dat file?
I wrote a batch file that quickly restores these files from a backup folder inside the
Settings folder, that file was included.
I don't have any played scenario at moment to test this theory.
Anyway, if this happens without any mod interference and maybe rather on updated game version/scenarios, then another entry for the everlasting to-fix list.

Should you cheat yourself again through the scenarios, I suggest to make also a
backup folder inside there (and also elsewhere on a backup disc/drive) to quickly restore your old settings. Always useful if you change computer or reinstall Windows. As long as the game won't forget the unlocks when quitting the game right away, it should be a good safety measure.
My batch file inside
Settings folder with link to desktop: