If the bootloader is borked how are you going to run fastboot commands?
firefirefire/u-boot is only the 2nd stage bootloader, there is a 1st stage bootloader which checks if there is something special on USB (factory cable, i think UART3 should work too btw.) does some small stuff and then go into fasboot mode (if special usb cable) or load the 2nd stage bootloader (u-boot) into RAM and jump into it. So if you have the factory cable plugged in the first stage bootloader should (?!?) handle it. Ah not sure now when i write these line, thought i thought it was this way.
Note: From my understanding it should work like this, but i've not tried it so better ask someone with more knowledge.
Btw: fattire has coded a (2nd stage) bootloader CyanoBoot based on u-boot. It does the multiboot (boot from internal memory/SDCard) right (they had part of it working before). There are differences between the B&N and Amazon u-boot (the nook has also more hardware keys) but it should not be too hard to port, is interested in porting have a closer look (source is here: http://goo-inside.me/devs/fattire/cyanoboot/acclaim/ )
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