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Yeah, but from that message there is obviously a process.

You're not supposed to ever use the bootloader reflash for multiple reasons. One of the main ones being that you can't actually get to the serial port without taking it apart and adding a RS232 level converter. Another is that there are multiple flash types with different programming algorithms. Hopefully you have a chip that is supported by the bootloader. If not then you'll have to desolder it and program it out of circuit.

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I'm actually hoping one of the guys who designed the little gems is still around and has kept the stuff "just in case".

Roger is actually one of the guys that designed it.