Hi,
There is a potential problem, I think, with Arduinos that have the USB Interface in another ATmel chip. Like current UNOs. I have heard that slow power down and glitches can corrupt the USB chip, and you would have to reload it.
I have also experienced this with older FTDI USB-based Arduinos. In that case the bootloader is corrupted and you need to re'burn' the bootloader. I saw this especially in classes where students were breadboarding stuff.
I'm not sure I have a good answer/solution. Other info or opinions wanted!