I found and read the manual of Misison Launcher in gamedir.
So, I assume when player starts mission with mod, Mission Launcher backing up original files, replaces them with mod-ones, then waiting when games finish to restore the backup.
And if player encounter power outage or Mission Launcher will be terminated while game running, next time when player launches the Mission Launcher, files wouldn’t be restored, because state is saved in-memory when Mission Launcher running.
I suggest to save the state on disk, in some file in gamedir, rather than keep it in memory, in this case if Mission Launcher accidently stops, at the next start it could read the state from that file and restore game content automatically, so it will eliminate the issue.