Well, I probably shouldn't be giving you advice since I haven't applied any of these change yet to my XT. But in reviewing the other thread, I see that there was a later version of the file that's used to change the boot flags to allow booting from the CF card. What was scanled.fir became bootflag.fir. In addition, its function was changed so that it toggles the bootflags to the opposite state each time you run it. See this message:
http://chdk.setepontos.com/index.php/topic,4202.msg40104.html#msg40104So it's possible if you install the bootflag.fir file the same way you did the scanled.fir file, it will reset the bootflags to their factory state. But if something is corrupted on your camera, installing bootflag.fir may only make things worse. As I understand it, you can still operate your camera so long as you have a bootable CF card installed. Maybe it would be best to just leave it that way.
I wish someone knowledgeable about this stuff could give you a solution. It would be comforting to know that all this stuff can be reversed if you want to do that for any reason.
