Thanks for the feedback.
I have also tried to reproduce it, by rebooting my device 5 times in a row and actually hoping that something would go wrong. But everything keeps working.
So really the only problem that crosses my mind that could have the potential to actually screw up functionality is the configuration file itself (/opt/amazon/ebook/bin/init.xargs). If this file is "wrong", it could potentially make the framework go weird. So just for completeness, here is how that file *should* look after the edit:
@tvjohn: did your edited file look like this? (I know you probably can't access it right now, so "from memory" is ok). Also, how did you edit that file? Directly on the device using vi or similar, or by copying it back and forth? If the latter, could it be that you used Mac line endings instead of Unix ones while saving?