It said that one file was "corrupted" and would be downloaded, which it did. When I started the game I found that all of my saved options had been reset to the default, so I'm thinking that the prefs.ini file is the one that was "corrupted".
Out of curiosity, I just checked this, though I'd validated immediately after patching. Found one file missing, and watching the game start up, it was indeed the pref file that is being replaced.
One thing I haven't been doing is loading a game from within the game, and after I ctrl-N and find a start location, I also exit and restart the game.