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What I'm wondering is why, if they know how to get executable code onto the player already, why they couldn't just turn around and send the bootloader code back out through that same interface. What is it about the player design which allows you to upload code to the player, but not be able to control the interface that you uploaded the code with?

It seems you "upload" the code by actually writing it to a partition on the iPod. As to why you can't just write it to another file *shrug*

Get some donations and get a sacrificial iPod. Open it up, dump the flash and then work out what is wired to what. Did it with the NSLU2 and all of the hardware has been worked out now.