Every update, or anything else that has the launcher verify the game files, is supposed to do that.
I've gone through two years of updates since starting my little "mod" project, and this has never happened until now. But I think that's because Steam used to handle the updates, not the launcher. This was the first time the launcher updated the game for me, and it nuked it.
The funny / sad thing is that I had a premonition something like this would happen (and
a plan to prepare for it), but stupid me got distracted forgot to back up those files. I have an earlier backup, the "public" version, but I had done some personal work since then that very likely is lost.
I'm not
that salty about it, because I knew I'd have to eventually redo everything for 4.0, but it has killed my interest in continuing with 3.8. My interest in 3.8 was very much on the fence anyway, ever since the announcement of "Legacy" mode and the cessation of community goals. Frontier just helped me with a little shove off that fence. Here I was worried about having to install an extra 50 GB, but instead I'll be freeing up 25 GB (at least for now).