I have solved with the method of deleting the options and version inis, then restarting, let the program rebuild the two files and editing "options.ini" to point to the correct mod directory. After doing this, there has been no rewrites.   Apparently though, I've cheered to soon.   There seem to be another issue, don't know if it's related. When using red side, the aircraft start at the same exact position in the sky, literally one inside the other, and explode.   I've read that it was an issue with some airports in some terrains, but this happens when starting the mission in the air. It also appears that the radio menu is messed up, like there is a "third squadron" but not a "second" in the list, and it doesn't reply to orders.   This game will never cease to amaze me.