arduino boards are extremely resillient, you'd be hard pushed to kill them for good, but it's possible to corrupt the bootloader, or flash them with code that has no apparent effect or that affects communication with the host.
Reflashing a bootloader requires a hardware programmer, or a suitable arduino board. I suspect you don't have either at hand?
If you can return the troublesome gemma I'm happy to have a look. If it's not dead, I can return it pre-burnt with the program you linked to if that's any use to you, i.e your deadlne has not passed.