Yes, I have had several instances of thses sorts of problems, as well. File managementhas been a pain in the rump, thus far. Now, (hopefully), I know better…I now have a folder called “Backups” in my etmain that has basically ALL my backups for radiant (further resubdivided accordingly…maps, scripts, textures…etc.
Now I just periodically drag all my stuff into there and overwrite the existing backup stuff. Files are (again, hopefully) safe from radiant scrutiny there.
