Sorry about the late reply;
Okay, checked out the persistent sfs file, every kerbal that is vanished with the exception of one scientist is missing from the file, I tried to approach one of the vanished kerbal ships but when you get to within 2.2 km KSP slows to a stop even when approaching on foot slowly you have to quickly back up or you will get stuck as the program will slow to around 15 to 30 seconds per frame, even if you get away KSP runs from then on in half speed.
I think that this particular save game has become corrupted somehow and will have to be deleted unfortunately.