When an engine crashes, you lose a lot of things that you shouldn't.
If you have something like session to session command line history, that doesn't happen. You obviously lose config settings or whatever video mode you might have selected.
FlashQuake saved the config any time you exit the menu.
Maybe session to session command line history should be perpetually saved every time a command is entered from the console. I can imagine that would stress out the engine, although to some degree it makes you wonder whether or not file append isn't a better option than the way it is currently written.
I do know that when a gamedir command is issued, the engine should save the config immediately before the gamedir change takes effect, otherwise you tend to have the odd situation where configuration changes you made get "lost" in some gamedir that isn't where they were intended to be.