I was assuming that he would get the images off the card by powering down for real, removing the card, transferring with a card reader, and re-inserting the card.
I think you are tackling the wrong problem here.
I was concerned about what happens when the tic timer "goes negative" or "wraps" if you just leave the camera running unattended. Reyalp has suggested that Canon (and the various CHDK devs) never intended or tested their code to run for months - never mind days.
So an occasional reset via script seemed like a good idea to get things reset. But not if it messes up image numbering.
Having said that ... as long as the OP periodically resets the camera while copying over saved images and deleting them, this does not seem like such a big problem.
Update : So, to make my question simple, ignore what has been posted in this thread so far. Here is what I want to do :1) Setup my CHDK camera to run an intervalometer script for a year unattended (external power supply on a UPS).
2) To avoid tic timer wrapping, buffer overruns, mallocs without free, stack creep, counter overruns and any other software bug that fouls up code that needs to run for a long time, I want the camera to automatically reset every day at 2 AM and then autostart the intervalometer script (that has been written knowing this will happen).
3) If I make sure the lens is parked ( playback mode plus a 2 minute delay ) then can I safely use the reboot() command without fear of image number corruption (assuming nobody has touched the camera since this process started) ??