The EEPROM on the GEMS board is a 29C256 and if/when it bricks itself (happens) you can reflash with whatever v1.xx .gin firmware file and go.
I've seriously considered reducing the GEMS board to FPGA and releasing it to the public. FPGA based 68HC11 emulations run ~2.5 time faster than any 68HC11, which is lolololol faster than v2.0 AEM. I'd probably be free to do so as long as i didn't profit - look closely, the AEMPro software has exactly zero copyrights.
As Jared Karagen's father lectured him about, reverse engineering anything is stupid and reverse engineering something without pay is fucking retarded. He has an essay on the subject typed up on pgmfi.org, and reading it was a turning point in my life. Jared's still all about it, but I very much see his old man's wisdom. I've reversed hardware and will continue to do it for simple things (GEMS "AEM" is very straightforward and honestly enjoyable to reverse, I hope for many such pieces of hardware until I've taken my hardware knowledge past *needing* to do such things) but taking on a whole EMS that I can't even profit off of isn't going to happen. I may or may not design one myself in the future, hardware is getting so powerful for the dollar that you can write sloppy code in VB and have a world class EMS if you know what you are about.
On that subject, makes me excited about what Fred's doing.