All ISP programming starts with a "Chip Erase" command that will wipe out the bootloader as well as an previous sketch.
I had a chip go dead that was recovered by re-installing the bootloader with a real STK-500. I don't recall what it had been running...
So I think we're still at the stage where "people think that this has happened", "it shouldn't be possible for it to happen", and "no one has identified a probable cause or demonstration sketch."
It is interesting that it doesn't seem to happen as often as it used to. All that's changed is the chip, the bootloader, the core libraries, and the IDE... 