Wow, I didn't even know this was possible
. I'm really surprised it doesn't even give any warnings, or outright crash (I just loaded it to see, too--same here).
A save isn't corruptible from within the game itself, but apparently it's possible that something happened at exactly the right (=bad) time when the OS was accessing the files. Also sounds like the way you dealt with it should have avoided any problem as I see it, though.
I'll have to look more into this after the 3c release, though I'll be really busy for the next couple days with that plus the event to begin hopefully the day after. The best solution would be to simply prevent multiple instances, since there's no reason for them.
I'm assuming nothing can save this particular game now, sorry
If it's any consolation, you'll get a new version in 12 hours, with some good tweaks for the latter half of the game...